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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: 11-125625919-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=125625919&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 125625919,
"ref": "G",
"alt": "T",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "ENST00000438015.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001114122.3",
"protein_id": "NP_001107594.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4128,
"mane_select": "ENST00000438015.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "ENST00000438015.7",
"protein_id": "ENSP00000388648.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4128,
"mane_select": "NM_001114122.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.159G>T",
"hgvs_p": "p.Ala53Ala",
"transcript": "ENST00000427383.6",
"protein_id": "ENSP00000391090.2",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 492,
"cds_start": 159,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 194,
"cdna_end": null,
"cdna_length": 1670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001114122.3",
"protein_id": "NP_001107594.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4128,
"mane_select": "ENST00000438015.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "ENST00000438015.7",
"protein_id": "ENSP00000388648.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4128,
"mane_select": "NM_001114122.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001114121.2",
"protein_id": "NP_001107593.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001244846.1",
"protein_id": "NP_001231775.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-193G>T",
"hgvs_p": null,
"transcript": "NM_001330427.2",
"protein_id": "NP_001317356.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 375,
"cds_start": -4,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.159G>T",
"hgvs_p": "p.Ala53Ala",
"transcript": "ENST00000711049.1",
"protein_id": "ENSP00000518558.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 492,
"cds_start": 159,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 237,
"cdna_end": null,
"cdna_length": 1912,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.159G>T",
"hgvs_p": "p.Ala53Ala",
"transcript": "XM_011542560.3",
"protein_id": "XP_011540862.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 492,
"cds_start": 159,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 3073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "n.159G>T",
"hgvs_p": null,
"transcript": "ENST00000525396.5",
"protein_id": "ENSP00000434141.2",
"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": 769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "n.784G>T",
"hgvs_p": null,
"transcript": "NR_045204.1",
"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": 3931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "n.784G>T",
"hgvs_p": null,
"transcript": "XR_007062447.1",
"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": 5615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001114121.2",
"protein_id": "NP_001107593.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "NM_001244846.1",
"protein_id": "NP_001231775.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 4053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-193G>T",
"hgvs_p": null,
"transcript": "NM_001330427.2",
"protein_id": "NP_001317356.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "ENST00000428830.6",
"protein_id": "ENSP00000412504.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 476,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1845,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-172G>T",
"hgvs_p": null,
"transcript": "ENST00000544373.5",
"protein_id": "ENSP00000442317.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 382,
"cds_start": -4,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
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"cdna_length": 1653,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "ENST00000278916.8",
"protein_id": "ENSP00000278916.4",
"transcript_support_level": 5,
"aa_start": null,
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"cdna_start": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-131G>T",
"hgvs_p": null,
"transcript": "ENST00000527013.6",
"protein_id": "ENSP00000431525.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-114G>T",
"hgvs_p": null,
"transcript": "ENST00000532669.5",
"protein_id": "ENSP00000434646.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-136G>T",
"hgvs_p": null,
"transcript": "ENST00000526937.5",
"protein_id": "ENSP00000431815.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": -4,
"cds_end": null,
"cds_length": 512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHEK1",
"gene_hgnc_id": 1925,
"hgvs_c": "c.-290G>T",
"hgvs_p": null,
"transcript": "ENST00000534685.5",
"protein_id": "ENSP00000432470.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 126,
"cds_start": -4,
"cds_end": null,
"cds_length": 381,
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},
{
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"canonical": false,
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"exon_count": 1,
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},
{
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},
{
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],
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"gene_symbol": "CHEK1",
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"hgvs_c": "c.-636G>T",
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"transcript": "XM_024448337.2",
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},
{
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],
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"gene_symbol": "CHEK1",
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}
],
"gene_symbol": "CHEK1",
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"dbsnp": "rs779165764",
"frequency_reference_population": 0.000021351583,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
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"gnomad_genomes_af": 0.0000591141,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6000000238418579,
"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": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.87,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000438015.7",
"gene_symbol": "CHEK1",
"hgnc_id": 1925,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-114G>T",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 5,
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"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NR_170378.1",
"gene_symbol": "LOC118567325",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-25C>A",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000686400.3",
"gene_symbol": "ENSG00000288907",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-1C>A",
"hgvs_p": null
}
],
"clinvar_disease": "CHEK1-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "CHEK1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}