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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: 2-232970265-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=232970265&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 232970265,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_019850.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "NM_019850.3",
"protein_id": "NP_062824.2",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 710,
"cds_start": 332,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264051.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019850.3"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "ENST00000264051.8",
"protein_id": "ENSP00000264051.3",
"transcript_support_level": 1,
"aa_start": 111,
"aa_end": null,
"aa_length": 710,
"cds_start": 332,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019850.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264051.8"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.431T>C",
"hgvs_p": "p.Met144Thr",
"transcript": "ENST00000905022.1",
"protein_id": "ENSP00000575081.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 743,
"cds_start": 431,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905022.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.431T>C",
"hgvs_p": "p.Met144Thr",
"transcript": "ENST00000965357.1",
"protein_id": "ENSP00000635416.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 743,
"cds_start": 431,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965357.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "ENST00000905023.1",
"protein_id": "ENSP00000575082.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 710,
"cds_start": 332,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905023.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "ENST00000965358.1",
"protein_id": "ENSP00000635417.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 710,
"cds_start": 332,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965358.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "ENST00000905024.1",
"protein_id": "ENSP00000575083.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 696,
"cds_start": 332,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905024.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.236T>C",
"hgvs_p": "p.Met79Thr",
"transcript": "ENST00000414326.1",
"protein_id": "ENSP00000405053.1",
"transcript_support_level": 2,
"aa_start": 79,
"aa_end": null,
"aa_length": 96,
"cds_start": 236,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414326.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr",
"transcript": "XM_011510923.4",
"protein_id": "XP_011509225.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 710,
"cds_start": 332,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510923.4"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000222001",
"gene_hgnc_id": null,
"hgvs_c": "n.68-42490A>G",
"hgvs_p": null,
"transcript": "ENST00000783807.1",
"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": "ENST00000783807.1"
}
],
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"dbsnp": "rs4973588",
"frequency_reference_population": 0.84997624,
"hom_count_reference_population": 581185,
"allele_count_reference_population": 1363707,
"gnomad_exomes_af": 0.848215,
"gnomad_genomes_af": 0.866788,
"gnomad_exomes_ac": 1231839,
"gnomad_genomes_ac": 131868,
"gnomad_exomes_homalt": 523810,
"gnomad_genomes_homalt": 57375,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 9.539071470499039e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.04,
"revel_prediction": "Benign",
"alphamissense_score": 0.0728,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.31,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_019850.3",
"gene_symbol": "NGEF",
"hgnc_id": 7807,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.332T>C",
"hgvs_p": "p.Met111Thr"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000783807.1",
"gene_symbol": "ENSG00000222001",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.68-42490A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}