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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: 16-75631490-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=75631490&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KARS1",
"hgnc_id": 6215,
"hgvs_c": "c.1262G>A",
"hgvs_p": "p.Arg421Gln",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_001130089.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 3476,
"alphamissense_prediction": null,
"alphamissense_score": 0.1477,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.03,
"chr": "16",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Charcot-Marie-Tooth disease recessive intermediate B,Hearing impairment,KARS1-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0507199764251709,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 597,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1991,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1178,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_005548.3",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1178G>A",
"hgvs_p": "p.Arg393Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000302445.8",
"protein_coding": true,
"protein_id": "NP_005539.1",
"strand": false,
"transcript": "NM_005548.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 597,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1991,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1178,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000302445.8",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1178G>A",
"hgvs_p": "p.Arg393Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005548.3",
"protein_coding": true,
"protein_id": "ENSP00000303043.3",
"strand": false,
"transcript": "ENST00000302445.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 625,
"aa_ref": "R",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2421,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000319410.9",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1262G>A",
"hgvs_p": "p.Arg421Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000325448.5",
"strand": false,
"transcript": "ENST00000319410.9",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 635,
"aa_ref": "R",
"aa_start": 431,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3103,
"cdna_start": 2316,
"cds_end": null,
"cds_length": 1908,
"cds_start": 1292,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000898534.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1292G>A",
"hgvs_p": "p.Arg431Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568593.1",
"strand": false,
"transcript": "ENST00000898534.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 633,
"aa_ref": "R",
"aa_start": 431,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2081,
"cdna_start": 1306,
"cds_end": null,
"cds_length": 1902,
"cds_start": 1292,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958942.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1292G>A",
"hgvs_p": "p.Arg431Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629001.1",
"strand": false,
"transcript": "ENST00000958942.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 625,
"aa_ref": "R",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2171,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001130089.2",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1262G>A",
"hgvs_p": "p.Arg421Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001123561.1",
"strand": false,
"transcript": "NM_001130089.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 598,
"aa_ref": "R",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1994,
"cdna_start": 1207,
"cds_end": null,
"cds_length": 1797,
"cds_start": 1181,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000898535.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Arg394Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568594.1",
"strand": false,
"transcript": "ENST00000898535.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 597,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2148,
"cdna_start": 1361,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1178,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000912463.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1178G>A",
"hgvs_p": "p.Arg393Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582522.1",
"strand": false,
"transcript": "ENST00000912463.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 595,
"aa_ref": "R",
"aa_start": 393,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2261,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 1788,
"cds_start": 1178,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000912464.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1178G>A",
"hgvs_p": "p.Arg393Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582523.1",
"strand": false,
"transcript": "ENST00000912464.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 557,
"aa_ref": "R",
"aa_start": 353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1863,
"cdna_start": 1084,
"cds_end": null,
"cds_length": 1674,
"cds_start": 1058,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000898537.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.1058G>A",
"hgvs_p": "p.Arg353Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568596.1",
"strand": false,
"transcript": "ENST00000898537.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 441,
"aa_ref": "R",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2105,
"cdna_start": 1318,
"cds_end": null,
"cds_length": 1326,
"cds_start": 710,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001378148.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.710G>A",
"hgvs_p": "p.Arg237Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365077.1",
"strand": false,
"transcript": "NM_001378148.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 366,
"aa_ref": "R",
"aa_start": 162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1291,
"cdna_start": 514,
"cds_end": null,
"cds_length": 1101,
"cds_start": 485,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000898536.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Arg162Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568595.1",
"strand": false,
"transcript": "ENST00000898536.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 109,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 527,
"cdna_start": null,
"cds_end": null,
"cds_length": 330,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000912465.1",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.112-2802G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582524.1",
"strand": false,
"transcript": "ENST00000912465.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 67,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 459,
"cdna_start": null,
"cds_end": null,
"cds_length": 204,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000568378.5",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "c.147-3501G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000454512.1",
"strand": false,
"transcript": "ENST00000568378.5",
"transcript_support_level": 5
},
{
"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": 1942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000564578.5",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "n.*721G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455818.1",
"strand": false,
"transcript": "ENST00000564578.5",
"transcript_support_level": 5
},
{
"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": 1942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000564578.5",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "n.*721G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455818.1",
"strand": false,
"transcript": "ENST00000564578.5",
"transcript_support_level": 5
},
{
"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": 801,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000562875.5",
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"hgvs_c": "n.*790G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456185.1",
"strand": true,
"transcript": "ENST00000562875.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149772470",
"effect": "missense_variant",
"frequency_reference_population": 0.0021534553,
"gene_hgnc_id": 6215,
"gene_symbol": "KARS1",
"gnomad_exomes_ac": 3239,
"gnomad_exomes_af": 0.00221566,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_ac": 237,
"gnomad_genomes_af": 0.00155634,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 6,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|not provided|Charcot-Marie-Tooth disease recessive intermediate B|Hearing impairment|KARS1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.417,
"pos": 75631490,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.729,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001130089.2"
}
]
}