← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 1-5887436-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=5887436&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 5887436,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000378156.9",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "NM_015102.5",
"protein_id": "NP_055917.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2555,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "ENST00000378156.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "ENST00000378156.9",
"protein_id": "ENSP00000367398.4",
"transcript_support_level": 1,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2555,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "NM_015102.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1236C>T",
"hgvs_p": null,
"transcript": "ENST00000378169.7",
"protein_id": "ENSP00000367411.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*149C>T",
"hgvs_p": null,
"transcript": "ENST00000466897.1",
"protein_id": "ENSP00000425745.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2332C>T",
"hgvs_p": null,
"transcript": "ENST00000489180.6",
"protein_id": "ENSP00000423747.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1236C>T",
"hgvs_p": null,
"transcript": "ENST00000378169.7",
"protein_id": "ENSP00000367411.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*149C>T",
"hgvs_p": null,
"transcript": "ENST00000466897.1",
"protein_id": "ENSP00000425745.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.799C>T",
"hgvs_p": "p.Gln267*",
"transcript": "NM_001291594.2",
"protein_id": "NP_001278523.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 914,
"cds_start": 799,
"cds_end": null,
"cds_length": 2745,
"cdna_start": 2068,
"cdna_end": null,
"cdna_length": 4468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.796C>T",
"hgvs_p": "p.Gln266*",
"transcript": "NM_001291593.2",
"protein_id": "NP_001278522.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 913,
"cds_start": 796,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 2245,
"cdna_end": null,
"cdna_length": 4645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Gln778*",
"transcript": "ENST00000622020.4",
"protein_id": "ENSP00000481831.2",
"transcript_support_level": 5,
"aa_start": 778,
"aa_end": null,
"aa_length": 911,
"cds_start": 2332,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2600,
"cdna_end": null,
"cdna_length": 3004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_006710563.4",
"protein_id": "XP_006710626.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2542,
"cdna_end": null,
"cdna_length": 4942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_011541216.3",
"protein_id": "XP_011539518.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 3093,
"cdna_end": null,
"cdna_length": 5493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_011541217.3",
"protein_id": "XP_011539519.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2957,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_047417535.1",
"protein_id": "XP_047273491.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 3082,
"cdna_end": null,
"cdna_length": 5482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_047417537.1",
"protein_id": "XP_047273493.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2691,
"cdna_end": null,
"cdna_length": 5091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_047417538.1",
"protein_id": "XP_047273494.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2991,
"cdna_end": null,
"cdna_length": 5391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_047417546.1",
"protein_id": "XP_047273502.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1426,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 2855,
"cdna_end": null,
"cdna_length": 5255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Gln778*",
"transcript": "XM_011541213.2",
"protein_id": "XP_011539515.1",
"transcript_support_level": null,
"aa_start": 778,
"aa_end": null,
"aa_length": 1425,
"cds_start": 2332,
"cds_end": null,
"cds_length": 4278,
"cdna_start": 2370,
"cdna_end": null,
"cdna_length": 4770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_011541214.2",
"protein_id": "XP_011539516.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1412,
"cds_start": 2335,
"cds_end": null,
"cds_length": 4239,
"cdna_start": 2373,
"cdna_end": null,
"cdna_length": 4731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Gln778*",
"transcript": "XM_017000996.2",
"protein_id": "XP_016856485.1",
"transcript_support_level": null,
"aa_start": 778,
"aa_end": null,
"aa_length": 1411,
"cds_start": 2332,
"cds_end": null,
"cds_length": 4236,
"cdna_start": 2370,
"cdna_end": null,
"cdna_length": 4728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2224C>T",
"hgvs_p": "p.Gln742*",
"transcript": "XM_011541215.2",
"protein_id": "XP_011539517.1",
"transcript_support_level": null,
"aa_start": 742,
"aa_end": null,
"aa_length": 1389,
"cds_start": 2224,
"cds_end": null,
"cds_length": 4170,
"cdna_start": 2262,
"cdna_end": null,
"cdna_length": 4662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_017000999.2",
"protein_id": "XP_016856488.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2460,
"cdna_end": null,
"cdna_length": 4860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_017001000.3",
"protein_id": "XP_016856489.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2196,
"cdna_end": null,
"cdna_length": 4596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417581.1",
"protein_id": "XP_047273537.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2998,
"cdna_end": null,
"cdna_length": 5398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417585.1",
"protein_id": "XP_047273541.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3065,
"cdna_end": null,
"cdna_length": 5465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417589.1",
"protein_id": "XP_047273545.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2987,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417590.1",
"protein_id": "XP_047273546.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2862,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417593.1",
"protein_id": "XP_047273549.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 6376,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1807C>T",
"hgvs_p": "p.Gln603*",
"transcript": "XM_047417599.1",
"protein_id": "XP_047273555.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 1250,
"cds_start": 1807,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 2760,
"cdna_end": null,
"cdna_length": 5160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_047417574.1",
"protein_id": "XP_047273530.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1235,
"cds_start": 2335,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 2373,
"cdna_end": null,
"cdna_length": 3846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_017000998.1",
"protein_id": "XP_016856487.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 1216,
"cds_start": 2335,
"cds_end": null,
"cds_length": 3651,
"cdna_start": 2373,
"cdna_end": null,
"cdna_length": 4269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1537C>T",
"hgvs_p": "p.Gln513*",
"transcript": "XM_017001001.2",
"protein_id": "XP_016856490.1",
"transcript_support_level": null,
"aa_start": 513,
"aa_end": null,
"aa_length": 1160,
"cds_start": 1537,
"cds_end": null,
"cds_length": 3483,
"cdna_start": 1640,
"cdna_end": null,
"cdna_length": 4040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.1534C>T",
"hgvs_p": "p.Gln512*",
"transcript": "XM_047417607.1",
"protein_id": "XP_047273563.1",
"transcript_support_level": null,
"aa_start": 512,
"aa_end": null,
"aa_length": 1159,
"cds_start": 1534,
"cds_end": null,
"cds_length": 3480,
"cdna_start": 1678,
"cdna_end": null,
"cdna_length": 4078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*",
"transcript": "XM_017001002.2",
"protein_id": "XP_016856491.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 939,
"cds_start": 2335,
"cds_end": null,
"cds_length": 2820,
"cdna_start": 2373,
"cdna_end": null,
"cdna_length": 4264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2174C>T",
"hgvs_p": "p.Ala725Val",
"transcript": "XM_047417617.1",
"protein_id": "XP_047273573.1",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 730,
"cds_start": 2174,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 2212,
"cdna_end": null,
"cdna_length": 2326,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2067C>T",
"hgvs_p": null,
"transcript": "ENST00000478423.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2552C>T",
"hgvs_p": null,
"transcript": "NR_111987.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2373C>T",
"hgvs_p": null,
"transcript": "XR_007058632.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2144-7197C>T",
"hgvs_p": null,
"transcript": "XM_047417555.1",
"protein_id": "XP_047273511.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1312,
"cds_start": -4,
"cds_end": null,
"cds_length": 3939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2141-7197C>T",
"hgvs_p": null,
"transcript": "XM_047417565.1",
"protein_id": "XP_047273521.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1311,
"cds_start": -4,
"cds_end": null,
"cds_length": 3936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"dbsnp": "rs137852922",
"frequency_reference_population": 0.0000041069165,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410692,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.550000011920929,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.879,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000378156.9",
"gene_symbol": "NPHP4",
"hgnc_id": 19104,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Gln779*"
}
],
"clinvar_disease": "Nephronophthisis,Senior-Loken syndrome 4",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Senior-Loken syndrome 4|Nephronophthisis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}