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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: 16-28986400-TGG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28986400&ref=TGG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28986400,
"ref": "TGG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000395456.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.268_269delGG",
"hgvs_p": "p.Gly90fs",
"transcript": "NM_001014987.2",
"protein_id": "NP_001014987.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 233,
"cds_start": 268,
"cds_end": null,
"cds_length": 702,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 1671,
"mane_select": "ENST00000395456.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.268_269delGG",
"hgvs_p": "p.Gly90fs",
"transcript": "ENST00000395456.7",
"protein_id": "ENSP00000378841.3",
"transcript_support_level": 1,
"aa_start": 90,
"aa_end": null,
"aa_length": 233,
"cds_start": 268,
"cds_end": null,
"cds_length": 702,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 1671,
"mane_select": "NM_001014987.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.376_377delGG",
"hgvs_p": "p.Gly126fs",
"transcript": "ENST00000395461.7",
"protein_id": "ENSP00000378845.3",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 269,
"cds_start": 376,
"cds_end": null,
"cds_length": 810,
"cdna_start": 412,
"cdna_end": null,
"cdna_length": 1448,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.265_266delGG",
"hgvs_p": "p.Gly89fs",
"transcript": "ENST00000566177.5",
"protein_id": "ENSP00000456761.1",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 261,
"cds_start": 265,
"cds_end": null,
"cds_length": 786,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.*37_*38delGG",
"hgvs_p": null,
"transcript": "ENST00000562701.5",
"protein_id": "ENSP00000454793.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.*37_*38delGG",
"hgvs_p": null,
"transcript": "ENST00000562701.5",
"protein_id": "ENSP00000454793.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.376_377delGG",
"hgvs_p": "p.Gly126fs",
"transcript": "NM_001014989.2",
"protein_id": "NP_001014989.2",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 269,
"cds_start": 376,
"cds_end": null,
"cds_length": 810,
"cdna_start": 435,
"cdna_end": null,
"cdna_length": 1472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.268_269delGG",
"hgvs_p": "p.Gly90fs",
"transcript": "NM_014387.4",
"protein_id": "NP_055202.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 262,
"cds_start": 268,
"cds_end": null,
"cds_length": 789,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 1758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.268_269delGG",
"hgvs_p": "p.Gly90fs",
"transcript": "ENST00000360872.9",
"protein_id": "ENSP00000354119.5",
"transcript_support_level": 2,
"aa_start": 90,
"aa_end": null,
"aa_length": 262,
"cds_start": 268,
"cds_end": null,
"cds_length": 789,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.265_266delGG",
"hgvs_p": "p.Gly89fs",
"transcript": "NM_001014988.2",
"protein_id": "NP_001014988.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 232,
"cds_start": 265,
"cds_end": null,
"cds_length": 699,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.265_266delGG",
"hgvs_p": "p.Gly89fs",
"transcript": "ENST00000454369.6",
"protein_id": "ENSP00000398793.2",
"transcript_support_level": 5,
"aa_start": 89,
"aa_end": null,
"aa_length": 232,
"cds_start": 265,
"cds_end": null,
"cds_length": 699,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 1262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.265_266delGG",
"hgvs_p": "p.Gly89fs",
"transcript": "ENST00000564277.5",
"protein_id": "ENSP00000457036.1",
"transcript_support_level": 5,
"aa_start": 89,
"aa_end": null,
"aa_length": 232,
"cds_start": 265,
"cds_end": null,
"cds_length": 699,
"cdna_start": 480,
"cdna_end": null,
"cdna_length": 921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "c.28_29delGG",
"hgvs_p": "p.Gly10fs",
"transcript": "ENST00000570232.2",
"protein_id": "ENSP00000455728.1",
"transcript_support_level": 5,
"aa_start": 10,
"aa_end": null,
"aa_length": 166,
"cds_start": 28,
"cds_end": null,
"cds_length": 501,
"cdna_start": 28,
"cdna_end": null,
"cdna_length": 707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.535_536delGG",
"hgvs_p": null,
"transcript": "ENST00000563964.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.306_307delGG",
"hgvs_p": null,
"transcript": "ENST00000568440.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.152_153delGG",
"hgvs_p": null,
"transcript": "ENST00000568899.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000261067",
"gene_hgnc_id": null,
"hgvs_c": "n.4181_4182delGG",
"hgvs_p": null,
"transcript": "ENST00000569969.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.521_522delGG",
"hgvs_p": null,
"transcript": "ENST00000697038.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.*99_*100delGG",
"hgvs_p": null,
"transcript": "ENST00000566270.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"hgvs_c": "n.*169_*170delGG",
"hgvs_p": null,
"transcript": "ENST00000562472.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAT",
"gene_hgnc_id": 18874,
"dbsnp": "rs781410769",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.291,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000395456.7",
"gene_symbol": "LAT",
"hgnc_id": 18874,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.268_269delGG",
"hgvs_p": "p.Gly90fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000569969.5",
"gene_symbol": "ENSG00000261067",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.4181_4182delGG",
"hgvs_p": null
}
],
"clinvar_disease": "Severe combined immunodeficiency due to LAT deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Severe combined immunodeficiency due to LAT deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}