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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: 5-80654922-GCCCCCAGCT-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=80654922&ref=GCCCCCAGCT&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 80654922,
"ref": "GCCCCCAGCT",
"alt": "G",
"effect": "conservative_inframe_deletion",
"transcript": "NM_002439.5",
"consequences": [
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "NM_002439.5",
"protein_id": "NP_002430.3",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1137,
"cds_start": 199,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265081.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002439.5"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000265081.7",
"protein_id": "ENSP00000265081.6",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 1137,
"cds_start": 199,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002439.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265081.7"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000667069.1",
"protein_id": "ENSP00000499502.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1072,
"cds_start": 199,
"cds_end": null,
"cds_length": 3219,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000667069.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-442_-434delAGCTGGGGG",
"hgvs_p": null,
"transcript": "NM_000791.4",
"protein_id": "NP_000782.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000439211.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000791.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-442_-434delAGCTGGGGG",
"hgvs_p": null,
"transcript": "ENST00000439211.7",
"protein_id": "ENSP00000396308.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000791.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439211.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.199_207delCCAGCTCCC",
"hgvs_p": null,
"transcript": "ENST00000670357.1",
"protein_id": "ENSP00000499791.1",
"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": "ENST00000670357.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000875834.1",
"protein_id": "ENSP00000545893.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1158,
"cds_start": 199,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875834.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000969134.1",
"protein_id": "ENSP00000639193.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1105,
"cds_start": 199,
"cds_end": null,
"cds_length": 3318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969134.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000875835.1",
"protein_id": "ENSP00000545894.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1056,
"cds_start": 199,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875835.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000933917.1",
"protein_id": "ENSP00000603976.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1033,
"cds_start": 199,
"cds_end": null,
"cds_length": 3102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933917.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000875836.1",
"protein_id": "ENSP00000545895.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 884,
"cds_start": 199,
"cds_end": null,
"cds_length": 2655,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875836.1"
},
{
"aa_ref": "PAP",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del",
"transcript": "ENST00000969133.1",
"protein_id": "ENSP00000639192.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 813,
"cds_start": 199,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969133.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-548_-540delAGCTGGGGG",
"hgvs_p": null,
"transcript": "NM_001290354.2",
"protein_id": "NP_001277283.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": null,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290354.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-442_-434delAGCTGGGGG",
"hgvs_p": null,
"transcript": "NM_001290357.2",
"protein_id": "NP_001277286.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": null,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001290357.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "n.53_61delAGCTGGGGG",
"hgvs_p": null,
"transcript": "NR_110936.2",
"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": "NR_110936.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.-271_-263delCCCCCAGCT",
"hgvs_p": null,
"transcript": "ENST00000658259.1",
"protein_id": "ENSP00000499617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1081,
"cds_start": null,
"cds_end": null,
"cds_length": 3246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000658259.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DHFR",
"gene_hgnc_id": 2861,
"hgvs_c": "c.-442_-434delAGCTGGGGG",
"hgvs_p": null,
"transcript": "ENST00000505337.5",
"protein_id": "ENSP00000426474.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 187,
"cds_start": null,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505337.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.-229_-221delCCCCCAGCT",
"hgvs_p": null,
"transcript": "ENST00000512531.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000512531.1"
}
],
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"dbsnp": "rs3045983",
"frequency_reference_population": 0.27090225,
"hom_count_reference_population": 63065,
"allele_count_reference_population": 412194,
"gnomad_exomes_af": 0.27234,
"gnomad_genomes_af": 0.257857,
"gnomad_exomes_ac": 373255,
"gnomad_genomes_ac": 38939,
"gnomad_exomes_homalt": 57880,
"gnomad_genomes_homalt": 5185,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.064,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PM4,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PM4",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002439.5",
"gene_symbol": "MSH3",
"hgnc_id": 7326,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.199_207delCCAGCTCCC",
"hgvs_p": "p.Pro67_Pro69del"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000791.4",
"gene_symbol": "DHFR",
"hgnc_id": 2861,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-442_-434delAGCTGGGGG",
"hgvs_p": null
}
],
"clinvar_disease": "Endometrial carcinoma,Familial adenomatous polyposis 4,Hereditary cancer-predisposing syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|not provided|Hereditary cancer-predisposing syndrome|Familial adenomatous polyposis 4;Endometrial carcinoma",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}