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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: 10-58385582-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=58385582&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TFAM",
"hgnc_id": 11741,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_003201.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.1513,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"chr": "10",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0754760205745697,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 246,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5025,
"cdna_start": 173,
"cds_end": null,
"cds_length": 741,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_003201.3",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000487519.6",
"protein_coding": true,
"protein_id": "NP_003192.1",
"strand": true,
"transcript": "NM_003201.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 246,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5025,
"cdna_start": 173,
"cds_end": null,
"cds_length": 741,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000487519.6",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003201.3",
"protein_coding": true,
"protein_id": "ENSP00000420588.1",
"strand": true,
"transcript": "ENST00000487519.6",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 241,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1928,
"cdna_start": 173,
"cds_end": null,
"cds_length": 726,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000909231.1",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579290.1",
"strand": true,
"transcript": "ENST00000909231.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 240,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1929,
"cdna_start": 177,
"cds_end": null,
"cds_length": 723,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000935269.1",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605328.1",
"strand": true,
"transcript": "ENST00000935269.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 214,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4929,
"cdna_start": 173,
"cds_end": null,
"cds_length": 645,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001270782.2",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001257711.1",
"strand": true,
"transcript": "NM_001270782.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 214,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 973,
"cdna_start": 149,
"cds_end": null,
"cds_length": 645,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000373895.7",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363002.3",
"strand": true,
"transcript": "ENST00000373895.7",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 208,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1829,
"cdna_start": 173,
"cds_end": null,
"cds_length": 627,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000935270.1",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605329.1",
"strand": true,
"transcript": "ENST00000935270.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 149,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 671,
"cdna_start": 173,
"cds_end": null,
"cds_length": 450,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047425697.1",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047281653.1",
"strand": true,
"transcript": "XM_047425697.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 148,
"aa_ref": "S",
"aa_start": 12,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 668,
"cdna_start": 173,
"cds_end": null,
"cds_length": 447,
"cds_start": 35,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_011540121.4",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Ser12Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011538423.1",
"strand": true,
"transcript": "XM_011540121.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1121,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000373899.3",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "n.238G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000373899.3",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5092,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_073073.2",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "n.173G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_073073.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 218,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 663,
"cdna_start": null,
"cds_end": null,
"cds_length": 657,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000395377.2",
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"hgvs_c": "c.-23G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378776.2",
"strand": true,
"transcript": "ENST00000395377.2",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1937",
"effect": "missense_variant",
"frequency_reference_population": 0.0000014096777,
"gene_hgnc_id": 11741,
"gene_symbol": "TFAM",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000140968,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.569,
"pos": 58385582,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.039,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003201.3"
}
]
}