← Back to variant description
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: 3-196323912-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196323912&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196323912,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_138461.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.535G>A",
"hgvs_p": "p.Ala179Thr",
"transcript": "NM_138461.4",
"protein_id": "NP_612470.2",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 209,
"cds_start": 535,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000273695.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138461.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.535G>A",
"hgvs_p": "p.Ala179Thr",
"transcript": "ENST00000273695.4",
"protein_id": "ENSP00000273695.4",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 209,
"cds_start": 535,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138461.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000273695.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.457G>A",
"hgvs_p": "p.Ala153Thr",
"transcript": "ENST00000454715.5",
"protein_id": "ENSP00000387728.1",
"transcript_support_level": 1,
"aa_start": 153,
"aa_end": null,
"aa_length": 183,
"cds_start": 457,
"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": "ENST00000454715.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.531G>A",
"hgvs_p": "p.Pro177Pro",
"transcript": "ENST00000446879.5",
"protein_id": "ENSP00000395280.1",
"transcript_support_level": 1,
"aa_start": 177,
"aa_end": null,
"aa_length": 299,
"cds_start": 531,
"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": "ENST00000446879.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-DYNLT2B",
"gene_hgnc_id": 49190,
"hgvs_c": "n.535G>A",
"hgvs_p": null,
"transcript": "ENST00000442633.1",
"protein_id": "ENSP00000405973.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000442633.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.457G>A",
"hgvs_p": "p.Ala153Thr",
"transcript": "NM_001204898.2",
"protein_id": "NP_001191827.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 183,
"cds_start": 457,
"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_001204898.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.531G>A",
"hgvs_p": "p.Pro177Pro",
"transcript": "NM_001204897.2",
"protein_id": "NP_001191826.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 242,
"cds_start": 531,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204897.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"hgvs_c": "c.132G>A",
"hgvs_p": "p.Pro44Pro",
"transcript": "ENST00000440822.2",
"protein_id": "ENSP00000414864.1",
"transcript_support_level": 3,
"aa_start": 44,
"aa_end": null,
"aa_length": 109,
"cds_start": 132,
"cds_end": null,
"cds_length": 330,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440822.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-AS1",
"gene_hgnc_id": 41085,
"hgvs_c": "n.273C>T",
"hgvs_p": null,
"transcript": "ENST00000444939.2",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000444939.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-AS1",
"gene_hgnc_id": 41085,
"hgvs_c": "n.185C>T",
"hgvs_p": null,
"transcript": "ENST00000452051.2",
"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": "pseudogene",
"feature": "ENST00000452051.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-DYNLT2B",
"gene_hgnc_id": 49190,
"hgvs_c": "n.693G>A",
"hgvs_p": null,
"transcript": "NR_037950.1",
"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": "NR_037950.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-AS1",
"gene_hgnc_id": 41085,
"hgvs_c": "n.189C>T",
"hgvs_p": null,
"transcript": "NR_046724.1",
"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": "NR_046724.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-AS1",
"gene_hgnc_id": 41085,
"hgvs_c": "n.*233C>T",
"hgvs_p": null,
"transcript": "ENST00000420226.2",
"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": "pseudogene",
"feature": "ENST00000420226.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM4SF19-AS1",
"gene_hgnc_id": 41085,
"hgvs_c": "n.*239C>T",
"hgvs_p": null,
"transcript": "NR_121665.1",
"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": "NR_121665.1"
}
],
"gene_symbol": "TM4SF19",
"gene_hgnc_id": 25167,
"dbsnp": "rs368721054",
"frequency_reference_population": 0.000033459113,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000314664,
"gnomad_genomes_af": 0.0000526198,
"gnomad_exomes_ac": 46,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08079826831817627,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.027,
"revel_prediction": "Benign",
"alphamissense_score": 0.0686,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.92,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_138461.4",
"gene_symbol": "TM4SF19",
"hgnc_id": 25167,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.535G>A",
"hgvs_p": "p.Ala179Thr"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000442633.1",
"gene_symbol": "TM4SF19-DYNLT2B",
"hgnc_id": 49190,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.535G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000452051.2",
"gene_symbol": "TM4SF19-AS1",
"hgnc_id": 41085,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.185C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}