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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: 19-48334172-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48334172&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48334172,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_018273.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.1001A>G",
"hgvs_p": "p.Gln334Arg",
"transcript": "NM_018273.4",
"protein_id": "NP_060743.2",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 459,
"cds_start": 1001,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000293261.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018273.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.1001A>G",
"hgvs_p": "p.Gln334Arg",
"transcript": "ENST00000293261.8",
"protein_id": "ENSP00000293261.2",
"transcript_support_level": 1,
"aa_start": 334,
"aa_end": null,
"aa_length": 459,
"cds_start": 1001,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018273.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000293261.8"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.701A>G",
"hgvs_p": "p.Gln234Arg",
"transcript": "ENST00000377431.6",
"protein_id": "ENSP00000366649.1",
"transcript_support_level": 1,
"aa_start": 234,
"aa_end": null,
"aa_length": 359,
"cds_start": 701,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000377431.6"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Gln333Arg",
"transcript": "ENST00000948722.1",
"protein_id": "ENSP00000618781.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 458,
"cds_start": 998,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948722.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.995A>G",
"hgvs_p": "p.Gln332Arg",
"transcript": "ENST00000893975.1",
"protein_id": "ENSP00000564034.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 457,
"cds_start": 995,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893975.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.896A>G",
"hgvs_p": "p.Gln299Arg",
"transcript": "NM_001303538.2",
"protein_id": "NP_001290467.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 424,
"cds_start": 896,
"cds_end": null,
"cds_length": 1275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303538.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.896A>G",
"hgvs_p": "p.Gln299Arg",
"transcript": "ENST00000435956.7",
"protein_id": "ENSP00000397038.2",
"transcript_support_level": 2,
"aa_start": 299,
"aa_end": null,
"aa_length": 424,
"cds_start": 896,
"cds_end": null,
"cds_length": 1275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435956.7"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.893A>G",
"hgvs_p": "p.Gln298Arg",
"transcript": "ENST00000918864.1",
"protein_id": "ENSP00000588923.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 423,
"cds_start": 893,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918864.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.806A>G",
"hgvs_p": "p.Gln269Arg",
"transcript": "NM_001303539.2",
"protein_id": "NP_001290468.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 394,
"cds_start": 806,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303539.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.806A>G",
"hgvs_p": "p.Gln269Arg",
"transcript": "ENST00000893974.1",
"protein_id": "ENSP00000564033.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 394,
"cds_start": 806,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893974.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.701A>G",
"hgvs_p": "p.Gln234Arg",
"transcript": "NM_001303540.2",
"protein_id": "NP_001290469.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 359,
"cds_start": 701,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303540.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.590A>G",
"hgvs_p": "p.Gln197Arg",
"transcript": "ENST00000893977.1",
"protein_id": "ENSP00000564036.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 322,
"cds_start": 590,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893977.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.485A>G",
"hgvs_p": "p.Gln162Arg",
"transcript": "ENST00000893976.1",
"protein_id": "ENSP00000564035.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 287,
"cds_start": 485,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893976.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "c.395A>G",
"hgvs_p": "p.Gln132Arg",
"transcript": "ENST00000948723.1",
"protein_id": "ENSP00000618782.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 257,
"cds_start": 395,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948723.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "n.488A>G",
"hgvs_p": null,
"transcript": "ENST00000600816.1",
"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": "retained_intron",
"feature": "ENST00000600816.1"
},
{
"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": "TMEM143",
"gene_hgnc_id": 25603,
"hgvs_c": "n.675A>G",
"hgvs_p": null,
"transcript": "NR_130317.2",
"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_130317.2"
}
],
"gene_symbol": "TMEM143",
"gene_hgnc_id": 25603,
"dbsnp": "rs1169067572",
"frequency_reference_population": 6.880986e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.88099e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2608627676963806,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.166,
"revel_prediction": "Benign",
"alphamissense_score": 0.1063,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.489,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018273.4",
"gene_symbol": "TMEM143",
"hgnc_id": 25603,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1001A>G",
"hgvs_p": "p.Gln334Arg"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}