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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: 2-47466807-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47466807&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47466807,
"ref": "A",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001406674.1",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_000251.3",
"protein_id": "NP_000242.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 934,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000233146.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000251.3"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "ENST00000233146.7",
"protein_id": "ENSP00000233146.2",
"transcript_support_level": 1,
"aa_start": 554,
"aa_end": null,
"aa_length": 934,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000251.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000233146.7"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "ENST00000406134.5",
"protein_id": "ENSP00000384199.1",
"transcript_support_level": 1,
"aa_start": 554,
"aa_end": null,
"aa_length": 921,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000406134.5"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406674.1",
"protein_id": "NP_001393603.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 1014,
"cds_start": 1660,
"cds_end": null,
"cds_length": 3045,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406674.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406631.1",
"protein_id": "NP_001393560.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 979,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406631.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406632.1",
"protein_id": "NP_001393561.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 976,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2931,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406632.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406633.1",
"protein_id": "NP_001393562.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 975,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2928,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406633.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406634.1",
"protein_id": "NP_001393563.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 974,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2925,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406634.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406635.1",
"protein_id": "NP_001393564.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 969,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2910,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406635.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1627A>T",
"hgvs_p": "p.Ser543Cys",
"transcript": "NM_001406636.1",
"protein_id": "NP_001393565.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 958,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2877,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406636.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406637.1",
"protein_id": "NP_001393566.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 957,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2874,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406637.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1711A>T",
"hgvs_p": "p.Ser571Cys",
"transcript": "ENST00000918107.1",
"protein_id": "ENSP00000588166.1",
"transcript_support_level": null,
"aa_start": 571,
"aa_end": null,
"aa_length": 951,
"cds_start": 1711,
"cds_end": null,
"cds_length": 2856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918107.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1699A>T",
"hgvs_p": "p.Ser567Cys",
"transcript": "NM_001406638.1",
"protein_id": "NP_001393567.1",
"transcript_support_level": null,
"aa_start": 567,
"aa_end": null,
"aa_length": 947,
"cds_start": 1699,
"cds_end": null,
"cds_length": 2844,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406638.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1699A>T",
"hgvs_p": "p.Ser567Cys",
"transcript": "ENST00000946816.1",
"protein_id": "ENSP00000616875.1",
"transcript_support_level": null,
"aa_start": 567,
"aa_end": null,
"aa_length": 947,
"cds_start": 1699,
"cds_end": null,
"cds_length": 2844,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946816.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406639.1",
"protein_id": "NP_001393568.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 945,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406639.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406640.1",
"protein_id": "NP_001393569.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 945,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406640.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406641.1",
"protein_id": "NP_001393570.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 934,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406641.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "ENST00000910408.1",
"protein_id": "ENSP00000580467.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 934,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2805,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910408.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1657A>T",
"hgvs_p": "p.Ser553Cys",
"transcript": "ENST00000910409.1",
"protein_id": "ENSP00000580468.1",
"transcript_support_level": null,
"aa_start": 553,
"aa_end": null,
"aa_length": 933,
"cds_start": 1657,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910409.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "ENST00000918103.1",
"protein_id": "ENSP00000588162.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 931,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2796,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918103.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.1660A>T",
"hgvs_p": "p.Ser554Cys",
"transcript": "NM_001406642.1",
"protein_id": "NP_001393571.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 929,
"cds_start": 1660,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001406642.1"
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
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"splice_prediction_selected": "Pathogenic",
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"revel_prediction": "Pathogenic",
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"bayesdelnoaf_score": 0.15,
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"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.88,
"spliceai_max_prediction": "Pathogenic",
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"dbscsnv_ada_prediction": "Pathogenic",
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"acmg_classification": "Pathogenic",
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"acmg_by_gene": [
{
"score": 18,
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"pathogenic_score": 18,
"criteria": [
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"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
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"verdict": "Pathogenic",
"transcript": "NM_001406674.1",
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"effects": [
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"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Lynch syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}