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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: 5-6599947-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=6599947&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 6599947,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_017755.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2283G>A",
"hgvs_p": "p.Ala761Ala",
"transcript": "NM_017755.6",
"protein_id": "NP_060225.4",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 767,
"cds_start": 2283,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264670.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017755.6"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2283G>A",
"hgvs_p": "p.Ala761Ala",
"transcript": "ENST00000264670.11",
"protein_id": "ENSP00000264670.6",
"transcript_support_level": 1,
"aa_start": 761,
"aa_end": null,
"aa_length": 767,
"cds_start": 2283,
"cds_end": null,
"cds_length": 2304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017755.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264670.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "n.2852G>A",
"hgvs_p": null,
"transcript": "ENST00000505892.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000505892.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2307G>A",
"hgvs_p": "p.Ala769Ala",
"transcript": "ENST00000902915.1",
"protein_id": "ENSP00000572974.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 775,
"cds_start": 2307,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902915.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2304G>A",
"hgvs_p": "p.Ala768Ala",
"transcript": "ENST00000939214.1",
"protein_id": "ENSP00000609273.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 774,
"cds_start": 2304,
"cds_end": null,
"cds_length": 2325,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939214.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Ala759Ala",
"transcript": "ENST00000939216.1",
"protein_id": "ENSP00000609275.1",
"transcript_support_level": null,
"aa_start": 759,
"aa_end": null,
"aa_length": 765,
"cds_start": 2277,
"cds_end": null,
"cds_length": 2298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939216.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2265G>A",
"hgvs_p": "p.Ala755Ala",
"transcript": "ENST00000902922.1",
"protein_id": "ENSP00000572981.1",
"transcript_support_level": null,
"aa_start": 755,
"aa_end": null,
"aa_length": 761,
"cds_start": 2265,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902922.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2265G>A",
"hgvs_p": "p.Ala755Ala",
"transcript": "ENST00000940950.1",
"protein_id": "ENSP00000611009.1",
"transcript_support_level": null,
"aa_start": 755,
"aa_end": null,
"aa_length": 761,
"cds_start": 2265,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940950.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2250G>A",
"hgvs_p": "p.Ala750Ala",
"transcript": "ENST00000902914.1",
"protein_id": "ENSP00000572973.1",
"transcript_support_level": null,
"aa_start": 750,
"aa_end": null,
"aa_length": 756,
"cds_start": 2250,
"cds_end": null,
"cds_length": 2271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902914.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2199G>A",
"hgvs_p": "p.Ala733Ala",
"transcript": "ENST00000902920.1",
"protein_id": "ENSP00000572979.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 739,
"cds_start": 2199,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902920.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2190G>A",
"hgvs_p": "p.Ala730Ala",
"transcript": "ENST00000902913.1",
"protein_id": "ENSP00000572972.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 736,
"cds_start": 2190,
"cds_end": null,
"cds_length": 2211,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902913.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2178G>A",
"hgvs_p": "p.Ala726Ala",
"transcript": "NM_001193455.2",
"protein_id": "NP_001180384.1",
"transcript_support_level": null,
"aa_start": 726,
"aa_end": null,
"aa_length": 732,
"cds_start": 2178,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193455.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2178G>A",
"hgvs_p": "p.Ala726Ala",
"transcript": "ENST00000506139.5",
"protein_id": "ENSP00000420957.1",
"transcript_support_level": 2,
"aa_start": 726,
"aa_end": null,
"aa_length": 732,
"cds_start": 2178,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506139.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2172G>A",
"hgvs_p": "p.Ala724Ala",
"transcript": "ENST00000939217.1",
"protein_id": "ENSP00000609276.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 730,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2193,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939217.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2160G>A",
"hgvs_p": "p.Ala720Ala",
"transcript": "ENST00000939215.1",
"protein_id": "ENSP00000609274.1",
"transcript_support_level": null,
"aa_start": 720,
"aa_end": null,
"aa_length": 726,
"cds_start": 2160,
"cds_end": null,
"cds_length": 2181,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939215.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.2145G>A",
"hgvs_p": "p.Ala715Ala",
"transcript": "ENST00000902918.1",
"protein_id": "ENSP00000572977.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 721,
"cds_start": 2145,
"cds_end": null,
"cds_length": 2166,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902918.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.1869G>A",
"hgvs_p": "p.Ala623Ala",
"transcript": "ENST00000902917.1",
"protein_id": "ENSP00000572976.1",
"transcript_support_level": null,
"aa_start": 623,
"aa_end": null,
"aa_length": 629,
"cds_start": 1869,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902917.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.1722G>A",
"hgvs_p": "p.Ala574Ala",
"transcript": "ENST00000902916.1",
"protein_id": "ENSP00000572975.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 580,
"cds_start": 1722,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902916.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.1647G>A",
"hgvs_p": "p.Ala549Ala",
"transcript": "ENST00000902921.1",
"protein_id": "ENSP00000572980.1",
"transcript_support_level": null,
"aa_start": 549,
"aa_end": null,
"aa_length": 555,
"cds_start": 1647,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902921.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "c.1641G>A",
"hgvs_p": "p.Ala547Ala",
"transcript": "ENST00000902919.1",
"protein_id": "ENSP00000572978.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 553,
"cds_start": 1641,
"cds_end": null,
"cds_length": 1662,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902919.1"
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "n.*1589G>A",
"hgvs_p": null,
"transcript": "ENST00000504374.5",
"protein_id": "ENSP00000421783.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504374.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "n.743G>A",
"hgvs_p": null,
"transcript": "ENST00000513888.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000513888.5"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
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"exon_count": 18,
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"intron_rank_end": null,
"gene_symbol": "NSUN2",
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"hgvs_c": "n.2263G>A",
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"transcript": "NR_037947.2",
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"transcript_support_level": null,
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"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037947.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "n.*1589G>A",
"hgvs_p": null,
"transcript": "ENST00000504374.5",
"protein_id": "ENSP00000421783.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000504374.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LINC01018",
"gene_hgnc_id": 27394,
"hgvs_c": "n.775-174C>T",
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"transcript": "ENST00000661215.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000661215.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LINC01018",
"gene_hgnc_id": 27394,
"hgvs_c": "n.571-174C>T",
"hgvs_p": null,
"transcript": "ENST00000669289.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000669289.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LINC01018",
"gene_hgnc_id": 27394,
"hgvs_c": "n.720-13623C>T",
"hgvs_p": null,
"transcript": "ENST00000752507.1",
"protein_id": null,
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"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000752507.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"hgvs_c": "n.*389G>A",
"hgvs_p": null,
"transcript": "ENST00000514127.1",
"protein_id": "ENSP00000426459.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000514127.1"
}
],
"gene_symbol": "NSUN2",
"gene_hgnc_id": 25994,
"dbsnp": "rs752702755",
"frequency_reference_population": 0.00009111307,
"hom_count_reference_population": 0,
"allele_count_reference_population": 147,
"gnomad_exomes_af": 0.0000985541,
"gnomad_genomes_af": 0.0000197039,
"gnomad_exomes_ac": 144,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7699999809265137,
"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": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.731,
"phylop100way_prediction": "Benign",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_017755.6",
"gene_symbol": "NSUN2",
"hgnc_id": 25994,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2283G>A",
"hgvs_p": "p.Ala761Ala"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000661215.2",
"gene_symbol": "LINC01018",
"hgnc_id": 27394,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.775-174C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 5,Intellectual disability,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Intellectual disability, autosomal recessive 5|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}