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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: 3-196318053-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196318053&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DYNLT2B",
"hgnc_id": 28482,
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001351628.2",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000272741",
"hgnc_id": null,
"hgvs_c": "n.100G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000431391.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TM4SF19-DYNLT2B",
"hgnc_id": 49190,
"hgvs_c": "n.*74-1822G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000442633.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "TM4SF19-AS1",
"hgnc_id": 41085,
"hgvs_c": "n.-235C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000420226.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0826,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.76,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.05004417896270752,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 142,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 625,
"cdna_start": 188,
"cds_end": null,
"cds_length": 429,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_152773.5",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000325318.10",
"protein_coding": true,
"protein_id": "NP_689986.2",
"strand": false,
"transcript": "NM_152773.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 142,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 625,
"cdna_start": 188,
"cds_end": null,
"cds_length": 429,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000325318.10",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_152773.5",
"protein_coding": true,
"protein_id": "ENSP00000324323.5",
"strand": false,
"transcript": "ENST00000325318.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000431391.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000272741",
"hgvs_c": "n.100G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000405181.1",
"strand": false,
"transcript": "ENST00000431391.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 964,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000442633.1",
"gene_hgnc_id": 49190,
"gene_symbol": "TM4SF19-DYNLT2B",
"hgvs_c": "n.*74-1822G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000405973.1",
"strand": false,
"transcript": "ENST00000442633.1",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 200,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 752,
"cdna_start": 141,
"cds_end": null,
"cds_length": 603,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931284.1",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601343.1",
"strand": false,
"transcript": "ENST00000931284.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 165,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 686,
"cdna_start": 180,
"cds_end": null,
"cds_length": 498,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931283.1",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601342.1",
"strand": false,
"transcript": "ENST00000931283.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 161,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 752,
"cdna_start": 258,
"cds_end": null,
"cds_length": 486,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931282.1",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601341.1",
"strand": false,
"transcript": "ENST00000931282.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 148,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 620,
"cdna_start": 188,
"cds_end": null,
"cds_length": 447,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001351628.2",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001338557.1",
"strand": false,
"transcript": "NM_001351628.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 119,
"aa_ref": "V",
"aa_start": 34,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 548,
"cdna_start": 182,
"cds_end": null,
"cds_length": 360,
"cds_start": 100,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000943620.1",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "c.100G>A",
"hgvs_p": "p.Val34Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000613679.1",
"strand": false,
"transcript": "ENST00000943620.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000426563.5",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "n.100G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415835.1",
"strand": false,
"transcript": "ENST00000426563.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 800,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000446494.1",
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"hgvs_c": "n.100G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410605.1",
"strand": false,
"transcript": "ENST00000446494.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1008,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_037950.1",
"gene_hgnc_id": 49190,
"gene_symbol": "TM4SF19-DYNLT2B",
"hgvs_c": "n.862-1822G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_037950.1",
"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": 370,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000420226.2",
"gene_hgnc_id": 41085,
"gene_symbol": "TM4SF19-AS1",
"hgvs_c": "n.-235C>T",
"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": "ENST00000420226.2",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs748300114",
"effect": "missense_variant",
"frequency_reference_population": 0.000006578601,
"gene_hgnc_id": 28482,
"gene_symbol": "DYNLT2B",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065786,
"gnomad_genomes_homalt": 0,
"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": -1.35,
"pos": 196318053,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.068,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001351628.2"
}
]
}