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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: 5-76298918-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=76298918&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 76298918,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014979.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "NM_014979.4",
"protein_id": "NP_055794.3",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 727,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000502798.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014979.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "ENST00000502798.7",
"protein_id": "ENSP00000423541.2",
"transcript_support_level": 1,
"aa_start": 543,
"aa_end": null,
"aa_length": 727,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014979.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502798.7"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "NM_001297716.2",
"protein_id": "NP_001284645.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 676,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2031,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001297716.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "ENST00000322285.7",
"protein_id": "ENSP00000316983.7",
"transcript_support_level": 2,
"aa_start": 543,
"aa_end": null,
"aa_length": 676,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2031,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322285.7"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "XM_011543281.4",
"protein_id": "XP_011541583.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 727,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543281.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn",
"transcript": "XM_011543282.4",
"protein_id": "XP_011541584.2",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 727,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543282.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"hgvs_c": "c.592G>A",
"hgvs_p": "p.Asp198Asn",
"transcript": "XM_017009244.3",
"protein_id": "XP_016864733.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 382,
"cds_start": 592,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009244.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SV2C-AS2",
"gene_hgnc_id": 58251,
"hgvs_c": "n.811-12115C>T",
"hgvs_p": null,
"transcript": "ENST00000502589.2",
"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": "ENST00000502589.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SV2C-AS2",
"gene_hgnc_id": 58251,
"hgvs_c": "n.509-12115C>T",
"hgvs_p": null,
"transcript": "ENST00000784363.1",
"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": "ENST00000784363.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SV2C-AS2",
"gene_hgnc_id": 58251,
"hgvs_c": "n.447-733C>T",
"hgvs_p": null,
"transcript": "XR_001742750.2",
"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": "XR_001742750.2"
}
],
"gene_symbol": "SV2C",
"gene_hgnc_id": 30670,
"dbsnp": "rs31244",
"frequency_reference_population": 0.08335564,
"hom_count_reference_population": 6155,
"allele_count_reference_population": 134488,
"gnomad_exomes_af": 0.0812816,
"gnomad_genomes_af": 0.103267,
"gnomad_exomes_ac": 118770,
"gnomad_genomes_ac": 15718,
"gnomad_exomes_homalt": 5286,
"gnomad_genomes_homalt": 869,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0015901029109954834,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.071,
"revel_prediction": "Benign",
"alphamissense_score": 0.0624,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.216,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_014979.4",
"gene_symbol": "SV2C",
"hgnc_id": 30670,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Asp543Asn"
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000784363.1",
"gene_symbol": "SV2C-AS2",
"hgnc_id": 58251,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.509-12115C>T",
"hgvs_p": null
}
],
"clinvar_disease": "SV2C-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SV2C-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}