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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: 5-149041467-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=149041467&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SH3TC2",
"hgnc_id": 29427,
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Arg227Gln",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_024577.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM5",
"acmg_score": 2,
"allele_count_reference_population": 9,
"alphamissense_prediction": null,
"alphamissense_score": 0.1115,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Charcot-Marie-Tooth disease,Charcot-Marie-Tooth disease type 4",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5532975792884827,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1288,
"aa_ref": "R",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 26468,
"cdna_start": 720,
"cds_end": null,
"cds_length": 3867,
"cds_start": 680,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_024577.4",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Arg227Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000515425.6",
"protein_coding": true,
"protein_id": "NP_078853.2",
"strand": false,
"transcript": "NM_024577.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1288,
"aa_ref": "R",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 26468,
"cdna_start": 720,
"cds_end": null,
"cds_length": 3867,
"cds_start": 680,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000515425.6",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Arg227Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024577.4",
"protein_coding": true,
"protein_id": "ENSP00000423660.1",
"strand": false,
"transcript": "ENST00000515425.6",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1281,
"aa_ref": "R",
"aa_start": 220,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4002,
"cdna_start": 726,
"cds_end": null,
"cds_length": 3846,
"cds_start": 659,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000512049.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "c.659G>A",
"hgvs_p": "p.Arg220Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421860.1",
"strand": false,
"transcript": "ENST00000512049.5",
"transcript_support_level": 1
},
{
"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": 7324,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000323829.9",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.673+7G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000313025.5",
"strand": false,
"transcript": "ENST00000323829.9",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 1255,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4625,
"cdna_start": 676,
"cds_end": null,
"cds_length": 3768,
"cds_start": 581,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000964176.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "c.581G>A",
"hgvs_p": "p.Arg194Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634235.1",
"strand": false,
"transcript": "ENST00000964176.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 604,
"aa_ref": "R",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2856,
"cdna_start": 718,
"cds_end": null,
"cds_length": 1815,
"cds_start": 680,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000867060.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Arg227Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537119.1",
"strand": false,
"transcript": "ENST00000867060.1",
"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": 4153,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000504517.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.80G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421779.1",
"strand": false,
"transcript": "ENST00000504517.5",
"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": 4416,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000504690.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.680G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000425627.1",
"strand": false,
"transcript": "ENST00000504690.5",
"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": 3276,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000511307.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.*460G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421420.1",
"strand": false,
"transcript": "ENST00000511307.5",
"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": 9374,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000675793.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.680G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502039.1",
"strand": false,
"transcript": "ENST00000675793.1",
"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": 3276,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000511307.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.*460G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421420.1",
"strand": false,
"transcript": "ENST00000511307.5",
"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": 5474,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000502274.2",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.619+7G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421092.2",
"strand": false,
"transcript": "ENST00000502274.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 570,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000503071.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.198+7G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000503071.1",
"transcript_support_level": 4
},
{
"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": 4051,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000513604.5",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.673+7G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000423111.1",
"strand": false,
"transcript": "ENST00000513604.5",
"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": 3228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000674983.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.673+7G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000502387.1",
"strand": false,
"transcript": "ENST00000674983.1",
"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": 4379,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676056.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.673+7G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000501827.1",
"strand": false,
"transcript": "ENST00000676056.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1063,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676367.1",
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"hgvs_c": "n.289+7G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000676367.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1257812868",
"effect": "missense_variant",
"frequency_reference_population": 0.0000055769824,
"gene_hgnc_id": 29427,
"gene_symbol": "SH3TC2",
"gnomad_exomes_ac": 8,
"gnomad_exomes_af": 0.00000547351,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657073,
"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": "Uncertain significance",
"phenotype_combined": "Charcot-Marie-Tooth disease type 4|Charcot-Marie-Tooth disease",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.616,
"pos": 149041467,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.146,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_024577.4"
}
]
}