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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: 9-108874894-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=108874894&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 108874894,
"ref": "C",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_003640.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "NM_003640.5",
"protein_id": "NP_003631.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374647.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003640.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "ENST00000374647.10",
"protein_id": "ENSP00000363779.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003640.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374647.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.2884+1G>T",
"hgvs_p": null,
"transcript": "ENST00000537196.1",
"protein_id": "ENSP00000439367.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 983,
"cds_start": null,
"cds_end": null,
"cds_length": 2952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537196.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.*2541+1G>T",
"hgvs_p": null,
"transcript": "ENST00000495759.6",
"protein_id": "ENSP00000433514.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000495759.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3973+1G>T",
"hgvs_p": null,
"transcript": "ENST00000675825.1",
"protein_id": "ENSP00000502632.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1346,
"cds_start": null,
"cds_end": null,
"cds_length": 4041,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675825.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "ENST00000675052.1",
"protein_id": "ENSP00000502664.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1343,
"cds_start": null,
"cds_end": null,
"cds_length": 4032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675052.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "ENST00000675406.1",
"protein_id": "ENSP00000501893.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675406.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "ENST00000861104.1",
"protein_id": "ENSP00000531163.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861104.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null,
"transcript": "ENST00000933697.1",
"protein_id": "ENSP00000603756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1332,
"cds_start": null,
"cds_end": null,
"cds_length": 3999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933697.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3877+1G>T",
"hgvs_p": null,
"transcript": "ENST00000933696.1",
"protein_id": "ENSP00000603755.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1314,
"cds_start": null,
"cds_end": null,
"cds_length": 3945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933696.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3874+1G>T",
"hgvs_p": null,
"transcript": "ENST00000676237.1",
"protein_id": "ENSP00000501828.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1313,
"cds_start": null,
"cds_end": null,
"cds_length": 3942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676237.1"
},
{
"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": 36,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3855+3101G>T",
"hgvs_p": null,
"transcript": "ENST00000674535.1",
"protein_id": "ENSP00000502142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1302,
"cds_start": null,
"cds_end": null,
"cds_length": 3909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674535.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3631+1G>T",
"hgvs_p": null,
"transcript": "ENST00000676416.1",
"protein_id": "ENSP00000501660.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1232,
"cds_start": null,
"cds_end": null,
"cds_length": 3699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676416.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3589+1G>T",
"hgvs_p": null,
"transcript": "NM_001318360.2",
"protein_id": "NP_001305289.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1218,
"cds_start": null,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318360.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3589+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674938.1",
"protein_id": "ENSP00000502427.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1218,
"cds_start": null,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674938.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.3589+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674948.1",
"protein_id": "ENSP00000501602.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1218,
"cds_start": null,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674948.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 34,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "c.2884+1G>T",
"hgvs_p": null,
"transcript": "NM_001330749.2",
"protein_id": "NP_001317678.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 983,
"cds_start": null,
"cds_end": null,
"cds_length": 2952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330749.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.7016+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674704.1",
"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": "retained_intron",
"feature": "ENST00000674704.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.814+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674740.1",
"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": "ENST00000674740.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.4544+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674836.1",
"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": "retained_intron",
"feature": "ENST00000674836.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.*1166+1G>T",
"hgvs_p": null,
"transcript": "ENST00000674890.1",
"protein_id": "ENSP00000501870.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000674890.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"hgvs_c": "n.*134+1G>T",
"hgvs_p": null,
"transcript": "ENST00000675078.1",
"protein_id": "ENSP00000501549.1",
"transcript_support_level": null,
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{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 35,
"intron_rank": 34,
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"gene_symbol": "ELP1",
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"transcript": "ENST00000676086.1",
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"biotype": "retained_intron",
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{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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"intron_variant"
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"exon_rank": null,
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"exon_count": 35,
"intron_rank": 34,
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"gene_symbol": "ELP1",
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"hgvs_c": "n.5759+1G>T",
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"transcript": "ENST00000676121.1",
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"biotype": "retained_intron",
"feature": "ENST00000676121.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
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"exon_rank": null,
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"exon_count": 7,
"intron_rank": 6,
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"gene_symbol": "ELP1",
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"hgvs_c": "n.660+1G>T",
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"transcript": "ENST00000676162.1",
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"biotype": "pseudogene",
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{
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"intron_variant"
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"gene_symbol": "ELP1",
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"biotype": "retained_intron",
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{
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"splice_donor_variant",
"intron_variant"
],
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"gene_symbol": "ELP1",
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"hgvs_c": "n.8400+1G>T",
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"transcript": "ENST00000676429.1",
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"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000676429.1"
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],
"gene_symbol": "ELP1",
"gene_hgnc_id": 5959,
"dbsnp": "rs143674809",
"frequency_reference_population": 0.000021935404,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000138558,
"gnomad_genomes_af": 0.0000985817,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.18000000715255737,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.437,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999989263107695,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_003640.5",
"gene_symbol": "ELP1",
"hgnc_id": 5959,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3931+1G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Familial dysautonomia,Medulloblastoma,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Familial dysautonomia|not provided|not specified|Familial dysautonomia;Medulloblastoma",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}