← 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: 13-76995077-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=76995077&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 76995077,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_006493.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "NM_006493.4",
"protein_id": "NP_006484.2",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 358,
"cds_start": 188,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 5243,
"mane_select": "ENST00000377453.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000377453.9",
"protein_id": "ENSP00000366673.5",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 358,
"cds_start": 188,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 5243,
"mane_select": "NM_006493.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000636183.2",
"protein_id": "ENSP00000490181.2",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 358,
"cds_start": 188,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 1627,
"cdna_end": null,
"cdna_length": 6664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283208",
"gene_hgnc_id": null,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000638147.2",
"protein_id": "ENSP00000490953.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 201,
"cds_start": 188,
"cds_end": null,
"cds_length": 606,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 1863,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.23G>A",
"hgvs_p": "p.Arg8His",
"transcript": "ENST00000636705.1",
"protein_id": "ENSP00000490937.1",
"transcript_support_level": 5,
"aa_start": 8,
"aa_end": null,
"aa_length": 303,
"cds_start": 23,
"cds_end": null,
"cds_length": 912,
"cdna_start": 24,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000637397.2",
"protein_id": "ENSP00000490422.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 273,
"cds_start": 188,
"cds_end": null,
"cds_length": 822,
"cdna_start": 200,
"cdna_end": null,
"cdna_length": 5060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000636525.2",
"protein_id": "ENSP00000490078.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 270,
"cds_start": 188,
"cds_end": null,
"cds_length": 813,
"cdna_start": 191,
"cdna_end": null,
"cdna_length": 2508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000636767.2",
"protein_id": "ENSP00000489855.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 248,
"cds_start": 188,
"cds_end": null,
"cds_length": 747,
"cdna_start": 189,
"cdna_end": null,
"cdna_length": 2368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000616833.6",
"protein_id": "ENSP00000479547.3",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 207,
"cds_start": 188,
"cds_end": null,
"cds_length": 624,
"cdna_start": 196,
"cdna_end": null,
"cdna_length": 2527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "NM_001366624.2",
"protein_id": "NP_001353553.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 197,
"cds_start": 188,
"cds_end": null,
"cds_length": 594,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 5286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000636780.2",
"protein_id": "ENSP00000489809.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 197,
"cds_start": 188,
"cds_end": null,
"cds_length": 594,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 2683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000637537.2",
"protein_id": "ENSP00000489711.2",
"transcript_support_level": 4,
"aa_start": 63,
"aa_end": null,
"aa_length": 197,
"cds_start": 188,
"cds_end": null,
"cds_length": 594,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 2520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His",
"transcript": "ENST00000485938.4",
"protein_id": "ENSP00000482959.3",
"transcript_support_level": 2,
"aa_start": 63,
"aa_end": null,
"aa_length": 191,
"cds_start": 188,
"cds_end": null,
"cds_length": 576,
"cdna_start": 228,
"cdna_end": null,
"cdna_length": 2341,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.189G>A",
"hgvs_p": null,
"transcript": "ENST00000635905.1",
"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": 2791,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.125G>A",
"hgvs_p": null,
"transcript": "ENST00000635915.1",
"protein_id": "ENSP00000490560.1",
"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": 2517,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.198G>A",
"hgvs_p": null,
"transcript": "ENST00000635989.1",
"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": 604,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.1027G>A",
"hgvs_p": null,
"transcript": "ENST00000636520.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 5889,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.-68G>A",
"hgvs_p": null,
"transcript": "ENST00000636681.1",
"protein_id": "ENSP00000489922.1",
"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": 1791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.-68G>A",
"hgvs_p": null,
"transcript": "ENST00000636681.1",
"protein_id": "ENSP00000489922.1",
"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": 1791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "FBXL3",
"gene_hgnc_id": 13599,
"hgvs_c": "n.174-2126C>T",
"hgvs_p": null,
"transcript": "ENST00000485797.2",
"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": 527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.-152G>A",
"hgvs_p": null,
"transcript": "ENST00000636602.1",
"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": 661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.-160G>A",
"hgvs_p": null,
"transcript": "ENST00000637278.1",
"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": 2863,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"hgvs_c": "n.*210G>A",
"hgvs_p": null,
"transcript": "ENST00000636405.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 2511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLN5",
"gene_hgnc_id": 2076,
"dbsnp": "rs104894386",
"frequency_reference_population": 0.000009295235,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000889456,
"gnomad_genomes_af": 0.0000131439,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8017504215240479,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.85,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7441,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.982,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_006493.4",
"gene_symbol": "CLN5",
"hgnc_id": 2076,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His"
},
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM2",
"PM5",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000638147.2",
"gene_symbol": "ENSG00000283208",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.188G>A",
"hgvs_p": "p.Arg63His"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000485797.2",
"gene_symbol": "FBXL3",
"hgnc_id": 13599,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.174-2126C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Neuronal ceroid lipofuscinosis,Neuronal ceroid lipofuscinosis 5,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:3",
"phenotype_combined": "Neuronal ceroid lipofuscinosis 5|Neuronal ceroid lipofuscinosis|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}