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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: 15-31028454-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=31028454&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 31028454,
"ref": "A",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000256552.11",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3171T>A",
"hgvs_p": "p.Tyr1057*",
"transcript": "NM_001252024.2",
"protein_id": "NP_001238953.1",
"transcript_support_level": null,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1625,
"cds_start": 3171,
"cds_end": null,
"cds_length": 4878,
"cdna_start": 3323,
"cdna_end": null,
"cdna_length": 5787,
"mane_select": "ENST00000256552.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3171T>A",
"hgvs_p": "p.Tyr1057*",
"transcript": "ENST00000256552.11",
"protein_id": "ENSP00000256552.7",
"transcript_support_level": 1,
"aa_start": 1057,
"aa_end": null,
"aa_length": 1625,
"cds_start": 3171,
"cds_end": null,
"cds_length": 4878,
"cdna_start": 3323,
"cdna_end": null,
"cdna_length": 5787,
"mane_select": "NM_001252024.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3222T>A",
"hgvs_p": "p.Tyr1074*",
"transcript": "ENST00000558445.6",
"protein_id": "ENSP00000452946.2",
"transcript_support_level": 1,
"aa_start": 1074,
"aa_end": null,
"aa_length": 1642,
"cds_start": 3222,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 3423,
"cdna_end": null,
"cdna_length": 5887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3105T>A",
"hgvs_p": "p.Tyr1035*",
"transcript": "ENST00000397795.7",
"protein_id": "ENSP00000380897.2",
"transcript_support_level": 1,
"aa_start": 1035,
"aa_end": null,
"aa_length": 1603,
"cds_start": 3105,
"cds_end": null,
"cds_length": 4812,
"cdna_start": 3237,
"cdna_end": null,
"cdna_length": 5701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.2874T>A",
"hgvs_p": "p.Tyr958*",
"transcript": "ENST00000558768.5",
"protein_id": "ENSP00000453119.2",
"transcript_support_level": 1,
"aa_start": 958,
"aa_end": null,
"aa_length": 1526,
"cds_start": 2874,
"cds_end": null,
"cds_length": 4581,
"cdna_start": 2874,
"cdna_end": null,
"cdna_length": 4581,
"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": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "n.*2057T>A",
"hgvs_p": null,
"transcript": "ENST00000560801.5",
"protein_id": "ENSP00000453644.2",
"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": 4454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "n.*2057T>A",
"hgvs_p": null,
"transcript": "ENST00000560801.5",
"protein_id": "ENSP00000453644.2",
"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": 4454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3222T>A",
"hgvs_p": "p.Tyr1074*",
"transcript": "NM_001252020.2",
"protein_id": "NP_001238949.1",
"transcript_support_level": null,
"aa_start": 1074,
"aa_end": null,
"aa_length": 1642,
"cds_start": 3222,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 3423,
"cdna_end": null,
"cdna_length": 5887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3123T>A",
"hgvs_p": "p.Tyr1041*",
"transcript": "ENST00000711434.1",
"protein_id": "ENSP00000518752.1",
"transcript_support_level": null,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1609,
"cds_start": 3123,
"cds_end": null,
"cds_length": 4830,
"cdna_start": 3255,
"cdna_end": null,
"cdna_length": 5719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.3105T>A",
"hgvs_p": "p.Tyr1035*",
"transcript": "NM_002420.6",
"protein_id": "NP_002411.3",
"transcript_support_level": null,
"aa_start": 1035,
"aa_end": null,
"aa_length": 1603,
"cds_start": 3105,
"cds_end": null,
"cds_length": 4812,
"cdna_start": 3237,
"cdna_end": null,
"cdna_length": 5701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "c.567T>A",
"hgvs_p": "p.Tyr189*",
"transcript": "ENST00000559177.6",
"protein_id": "ENSP00000453477.2",
"transcript_support_level": 5,
"aa_start": 189,
"aa_end": null,
"aa_length": 757,
"cds_start": 567,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 567,
"cdna_end": null,
"cdna_length": 2274,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "n.546T>A",
"hgvs_p": null,
"transcript": "ENST00000557948.1",
"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": 564,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"hgvs_c": "n.394T>A",
"hgvs_p": null,
"transcript": "ENST00000558212.5",
"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": 670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259720",
"gene_hgnc_id": 58477,
"hgvs_c": "n.260+1343A>T",
"hgvs_p": null,
"transcript": "ENST00000558755.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259720",
"gene_hgnc_id": 58477,
"hgvs_c": "n.19-7299A>T",
"hgvs_p": null,
"transcript": "ENST00000561299.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ENSG00000259720",
"gene_hgnc_id": 58477,
"hgvs_c": "n.218+1343A>T",
"hgvs_p": null,
"transcript": "ENST00000665655.1",
"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": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "TRPM1-AS1",
"gene_hgnc_id": 58477,
"hgvs_c": "n.88+1343A>T",
"hgvs_p": null,
"transcript": "XR_007064555.1",
"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": 953,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TRPM1-AS1",
"gene_hgnc_id": 58477,
"hgvs_c": "n.278+1343A>T",
"hgvs_p": null,
"transcript": "XR_932055.2",
"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": 870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRPM1-AS1",
"gene_hgnc_id": 58477,
"hgvs_c": "n.240+1343A>T",
"hgvs_p": null,
"transcript": "XR_932056.2",
"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": 1143,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRPM1",
"gene_hgnc_id": 7146,
"dbsnp": "rs267607140",
"frequency_reference_population": 0.000012997603,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000129976,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.49000000953674316,
"computational_prediction_selected": "Pathogenic",
"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": 0.49,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.046,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000256552.11",
"gene_symbol": "TRPM1",
"hgnc_id": 7146,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3171T>A",
"hgvs_p": "p.Tyr1057*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000558755.1",
"gene_symbol": "ENSG00000259720",
"hgnc_id": 58477,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.260+1343A>T",
"hgvs_p": null
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_932055.2",
"gene_symbol": "TRPM1-AS1",
"hgnc_id": 58477,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.278+1343A>T",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital stationary night blindness 1C,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Congenital stationary night blindness 1C|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}