← 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: 1-5863916-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=5863916&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 5863916,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000378156.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "NM_015102.5",
"protein_id": "NP_055917.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4334,
"cdna_end": null,
"cdna_length": 4955,
"mane_select": "ENST00000378156.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "ENST00000378156.9",
"protein_id": "ENSP00000367398.4",
"transcript_support_level": 1,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4334,
"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": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*3015C>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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.2862C>T",
"hgvs_p": null,
"transcript": "ENST00000460696.1",
"protein_id": null,
"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": 3967,
"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": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1925C>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": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*3015C>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": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.*1925C>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": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2578C>T",
"hgvs_p": "p.Leu860Leu",
"transcript": "NM_001291594.2",
"protein_id": "NP_001278523.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 914,
"cds_start": 2578,
"cds_end": null,
"cds_length": 2745,
"cdna_start": 3847,
"cdna_end": null,
"cdna_length": 4468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.2575C>T",
"hgvs_p": "p.Leu859Leu",
"transcript": "NM_001291593.2",
"protein_id": "NP_001278522.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 913,
"cds_start": 2575,
"cds_end": null,
"cds_length": 2742,
"cdna_start": 4024,
"cdna_end": null,
"cdna_length": 4645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_006710563.4",
"protein_id": "XP_006710626.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4321,
"cdna_end": null,
"cdna_length": 4942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_011541216.3",
"protein_id": "XP_011539518.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4872,
"cdna_end": null,
"cdna_length": 5493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_011541217.3",
"protein_id": "XP_011539519.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4736,
"cdna_end": null,
"cdna_length": 5357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_047417535.1",
"protein_id": "XP_047273491.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4861,
"cdna_end": null,
"cdna_length": 5482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_047417537.1",
"protein_id": "XP_047273493.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4470,
"cdna_end": null,
"cdna_length": 5091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_047417538.1",
"protein_id": "XP_047273494.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4770,
"cdna_end": null,
"cdna_length": 5391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu",
"transcript": "XM_047417546.1",
"protein_id": "XP_047273502.1",
"transcript_support_level": null,
"aa_start": 1372,
"aa_end": null,
"aa_length": 1426,
"cds_start": 4114,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4634,
"cdna_end": null,
"cdna_length": 5255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4111C>T",
"hgvs_p": "p.Leu1371Leu",
"transcript": "XM_011541213.2",
"protein_id": "XP_011539515.1",
"transcript_support_level": null,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1425,
"cds_start": 4111,
"cds_end": null,
"cds_length": 4278,
"cdna_start": 4149,
"cdna_end": null,
"cdna_length": 4770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4072C>T",
"hgvs_p": "p.Leu1358Leu",
"transcript": "XM_011541214.2",
"protein_id": "XP_011539516.1",
"transcript_support_level": null,
"aa_start": 1358,
"aa_end": null,
"aa_length": 1412,
"cds_start": 4072,
"cds_end": null,
"cds_length": 4239,
"cdna_start": 4110,
"cdna_end": null,
"cdna_length": 4731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4069C>T",
"hgvs_p": "p.Leu1357Leu",
"transcript": "XM_017000996.2",
"protein_id": "XP_016856485.1",
"transcript_support_level": null,
"aa_start": 1357,
"aa_end": null,
"aa_length": 1411,
"cds_start": 4069,
"cds_end": null,
"cds_length": 4236,
"cdna_start": 4107,
"cdna_end": null,
"cdna_length": 4728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.4003C>T",
"hgvs_p": "p.Leu1335Leu",
"transcript": "XM_011541215.2",
"protein_id": "XP_011539517.1",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 1389,
"cds_start": 4003,
"cds_end": null,
"cds_length": 4170,
"cdna_start": 4041,
"cdna_end": null,
"cdna_length": 4662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3772C>T",
"hgvs_p": "p.Leu1258Leu",
"transcript": "XM_047417555.1",
"protein_id": "XP_047273511.1",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1312,
"cds_start": 3772,
"cds_end": null,
"cds_length": 3939,
"cdna_start": 3810,
"cdna_end": null,
"cdna_length": 4431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3769C>T",
"hgvs_p": "p.Leu1257Leu",
"transcript": "XM_047417565.1",
"protein_id": "XP_047273521.1",
"transcript_support_level": null,
"aa_start": 1257,
"aa_end": null,
"aa_length": 1311,
"cds_start": 3769,
"cds_end": null,
"cds_length": 3936,
"cdna_start": 3807,
"cdna_end": null,
"cdna_length": 4428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_017000999.2",
"protein_id": "XP_016856488.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4239,
"cdna_end": null,
"cdna_length": 4860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_017001000.3",
"protein_id": "XP_016856489.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3975,
"cdna_end": null,
"cdna_length": 4596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417581.1",
"protein_id": "XP_047273537.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4777,
"cdna_end": null,
"cdna_length": 5398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417585.1",
"protein_id": "XP_047273541.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4844,
"cdna_end": null,
"cdna_length": 5465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417589.1",
"protein_id": "XP_047273545.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4766,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417590.1",
"protein_id": "XP_047273546.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4641,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417593.1",
"protein_id": "XP_047273549.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 8155,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3586C>T",
"hgvs_p": "p.Leu1196Leu",
"transcript": "XM_047417599.1",
"protein_id": "XP_047273555.1",
"transcript_support_level": null,
"aa_start": 1196,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3586,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 4539,
"cdna_end": null,
"cdna_length": 5160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3316C>T",
"hgvs_p": "p.Leu1106Leu",
"transcript": "XM_017001001.2",
"protein_id": "XP_016856490.1",
"transcript_support_level": null,
"aa_start": 1106,
"aa_end": null,
"aa_length": 1160,
"cds_start": 3316,
"cds_end": null,
"cds_length": 3483,
"cdna_start": 3419,
"cdna_end": null,
"cdna_length": 4040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "c.3313C>T",
"hgvs_p": "p.Leu1105Leu",
"transcript": "XM_047417607.1",
"protein_id": "XP_047273563.1",
"transcript_support_level": null,
"aa_start": 1105,
"aa_end": null,
"aa_length": 1159,
"cds_start": 3313,
"cds_end": null,
"cds_length": 3480,
"cdna_start": 3457,
"cdna_end": null,
"cdna_length": 4078,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.3265C>T",
"hgvs_p": null,
"transcript": "ENST00000378161.5",
"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": 4370,
"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": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.3846C>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": 32,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"hgvs_c": "n.4881C>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
}
],
"gene_symbol": "NPHP4",
"gene_hgnc_id": 19104,
"dbsnp": "rs374146357",
"frequency_reference_population": 0.00021190038,
"hom_count_reference_population": 0,
"allele_count_reference_population": 342,
"gnomad_exomes_af": 0.00017309,
"gnomad_genomes_af": 0.000584381,
"gnomad_exomes_ac": 253,
"gnomad_genomes_ac": 89,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4300000071525574,
"computational_prediction_selected": "Benign",
"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": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.598,
"phylop100way_prediction": "Pathogenic",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000378156.9",
"gene_symbol": "NPHP4",
"hgnc_id": 19104,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4114C>T",
"hgvs_p": "p.Leu1372Leu"
}
],
"clinvar_disease": "Nephronophthisis,Nephronophthisis 4,Senior-Loken syndrome 4,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Nephronophthisis|Senior-Loken syndrome 4|not provided|Nephronophthisis 4|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}