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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: 15-101646743-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=101646743&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 101646743,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_078474.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.484G>T",
"hgvs_p": "p.Asp162Tyr",
"transcript": "NM_078474.3",
"protein_id": "NP_510883.2",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 247,
"cds_start": 484,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000333202.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_078474.3"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.484G>T",
"hgvs_p": "p.Asp162Tyr",
"transcript": "ENST00000333202.8",
"protein_id": "ENSP00000330433.3",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 247,
"cds_start": 484,
"cds_end": null,
"cds_length": 744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_078474.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333202.8"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.406G>T",
"hgvs_p": "p.Asp136Tyr",
"transcript": "ENST00000347970.7",
"protein_id": "ENSP00000327584.3",
"transcript_support_level": 1,
"aa_start": 136,
"aa_end": null,
"aa_length": 221,
"cds_start": 406,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347970.7"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.406G>T",
"hgvs_p": "p.Asp136Tyr",
"transcript": "NM_025141.4",
"protein_id": "NP_079417.2",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 221,
"cds_start": 406,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025141.4"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.484G>T",
"hgvs_p": "p.Asp162Tyr",
"transcript": "NM_001308026.2",
"protein_id": "NP_001294955.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 209,
"cds_start": 484,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308026.2"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.484G>T",
"hgvs_p": "p.Asp162Tyr",
"transcript": "ENST00000559107.5",
"protein_id": "ENSP00000454131.1",
"transcript_support_level": 3,
"aa_start": 162,
"aa_end": null,
"aa_length": 209,
"cds_start": 484,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000559107.5"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.343G>T",
"hgvs_p": "p.Asp115Tyr",
"transcript": "ENST00000896613.1",
"protein_id": "ENSP00000566672.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 200,
"cds_start": 343,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896613.1"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.406G>T",
"hgvs_p": "p.Asp136Tyr",
"transcript": "NM_001307960.2",
"protein_id": "NP_001294889.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 183,
"cds_start": 406,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001307960.2"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.406G>T",
"hgvs_p": "p.Asp136Tyr",
"transcript": "ENST00000428002.6",
"protein_id": "ENSP00000402179.2",
"transcript_support_level": 2,
"aa_start": 136,
"aa_end": null,
"aa_length": 183,
"cds_start": 406,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428002.6"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.289G>T",
"hgvs_p": "p.Asp97Tyr",
"transcript": "ENST00000561373.1",
"protein_id": "ENSP00000452823.1",
"transcript_support_level": 2,
"aa_start": 97,
"aa_end": null,
"aa_length": 182,
"cds_start": 289,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000561373.1"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.271G>T",
"hgvs_p": "p.Asp91Tyr",
"transcript": "ENST00000922193.1",
"protein_id": "ENSP00000592252.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 176,
"cds_start": 271,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922193.1"
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "c.313G>T",
"hgvs_p": "p.Asp105Tyr",
"transcript": "ENST00000558129.5",
"protein_id": "ENSP00000453990.1",
"transcript_support_level": 3,
"aa_start": 105,
"aa_end": null,
"aa_length": 160,
"cds_start": 313,
"cds_end": null,
"cds_length": 483,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000558129.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.*720G>T",
"hgvs_p": null,
"transcript": "ENST00000558677.5",
"protein_id": "ENSP00000456921.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000558677.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.505G>T",
"hgvs_p": null,
"transcript": "ENST00000559024.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000559024.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.*852G>T",
"hgvs_p": null,
"transcript": "ENST00000560013.5",
"protein_id": "ENSP00000453503.1",
"transcript_support_level": 2,
"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": "ENST00000560013.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.426G>T",
"hgvs_p": null,
"transcript": "ENST00000560910.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000560910.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.*720G>T",
"hgvs_p": null,
"transcript": "ENST00000558677.5",
"protein_id": "ENSP00000456921.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000558677.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"hgvs_c": "n.*852G>T",
"hgvs_p": null,
"transcript": "ENST00000560013.5",
"protein_id": "ENSP00000453503.1",
"transcript_support_level": 2,
"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": "ENST00000560013.5"
}
],
"gene_symbol": "TM2D3",
"gene_hgnc_id": 24128,
"dbsnp": "rs1170553941",
"frequency_reference_population": 0.000004104394,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410439,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7816317081451416,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.23999999463558197,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.259,
"revel_prediction": "Benign",
"alphamissense_score": 0.4762,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.893,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.24,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_078474.3",
"gene_symbol": "TM2D3",
"hgnc_id": 24128,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.484G>T",
"hgvs_p": "p.Asp162Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}