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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: 2-85542980-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=85542980&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 85542980,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005911.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.1031A>C",
"hgvs_p": "p.Glu344Ala",
"transcript": "NM_005911.6",
"protein_id": "NP_005902.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 395,
"cds_start": 1031,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000306434.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005911.6"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.1031A>C",
"hgvs_p": "p.Glu344Ala",
"transcript": "ENST00000306434.8",
"protein_id": "ENSP00000303147.3",
"transcript_support_level": 1,
"aa_start": 344,
"aa_end": null,
"aa_length": 395,
"cds_start": 1031,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005911.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000306434.8"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.842A>C",
"hgvs_p": "p.Glu281Ala",
"transcript": "ENST00000409017.1",
"protein_id": "ENSP00000386353.1",
"transcript_support_level": 1,
"aa_start": 281,
"aa_end": null,
"aa_length": 299,
"cds_start": 842,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409017.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "n.1200A>C",
"hgvs_p": null,
"transcript": "ENST00000481412.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000481412.5"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.1019A>C",
"hgvs_p": "p.Glu340Ala",
"transcript": "ENST00000881374.1",
"protein_id": "ENSP00000551433.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 391,
"cds_start": 1019,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881374.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.1013A>C",
"hgvs_p": "p.Glu338Ala",
"transcript": "ENST00000881376.1",
"protein_id": "ENSP00000551435.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 389,
"cds_start": 1013,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881376.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.965A>C",
"hgvs_p": "p.Glu322Ala",
"transcript": "ENST00000881371.1",
"protein_id": "ENSP00000551430.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 373,
"cds_start": 965,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881371.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.956A>C",
"hgvs_p": "p.Glu319Ala",
"transcript": "ENST00000881373.1",
"protein_id": "ENSP00000551432.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 370,
"cds_start": 956,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881373.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.908A>C",
"hgvs_p": "p.Glu303Ala",
"transcript": "ENST00000881372.1",
"protein_id": "ENSP00000551431.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 354,
"cds_start": 908,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881372.1"
},
{
"aa_ref": "E",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"hgvs_c": "c.830A>C",
"hgvs_p": "p.Glu277Ala",
"transcript": "ENST00000881375.1",
"protein_id": "ENSP00000551434.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 328,
"cds_start": 830,
"cds_end": null,
"cds_length": 987,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881375.1"
}
],
"gene_symbol": "MAT2A",
"gene_hgnc_id": 6904,
"dbsnp": "rs886039820",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8727606534957886,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.952,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.228,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.873,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.08,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_005911.6",
"gene_symbol": "MAT2A",
"hgnc_id": 6904,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1031A>C",
"hgvs_p": "p.Glu344Ala"
}
],
"clinvar_disease": "Familial thoracic aortic aneurysm and aortic dissection,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "not provided|Familial thoracic aortic aneurysm and aortic dissection",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}