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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: 13-49496036-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=49496036&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 49496036,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001040443.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "NM_001040443.3",
"protein_id": "NP_001035533.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 331,
"cds_start": 35,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000378319.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040443.3"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000378319.8",
"protein_id": "ENSP00000367570.3",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 331,
"cds_start": 35,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001040443.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378319.8"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000941732.1",
"protein_id": "ENSP00000611791.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 329,
"cds_start": 35,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941732.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000873990.1",
"protein_id": "ENSP00000544049.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 327,
"cds_start": 35,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873990.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000873989.1",
"protein_id": "ENSP00000544048.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 307,
"cds_start": 35,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873989.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.19T>A",
"hgvs_p": "p.Cys7Ser",
"transcript": "ENST00000426879.5",
"protein_id": "ENSP00000394883.1",
"transcript_support_level": 2,
"aa_start": 7,
"aa_end": null,
"aa_length": 285,
"cds_start": 19,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426879.5"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000941733.1",
"protein_id": "ENSP00000611792.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 249,
"cds_start": 35,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941733.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu",
"transcript": "ENST00000496623.5",
"protein_id": "ENSP00000483500.1",
"transcript_support_level": 2,
"aa_start": 12,
"aa_end": null,
"aa_length": 159,
"cds_start": 35,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000496623.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.-245T>A",
"hgvs_p": null,
"transcript": "NM_001040444.3",
"protein_id": "NP_001035534.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040444.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.-598T>A",
"hgvs_p": null,
"transcript": "NM_001419873.1",
"protein_id": "NP_001406802.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001419873.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.-632T>A",
"hgvs_p": null,
"transcript": "NM_001419874.1",
"protein_id": "NP_001406803.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001419874.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.-436T>A",
"hgvs_p": null,
"transcript": "NM_001419875.1",
"protein_id": "NP_001406804.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001419875.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.-470T>A",
"hgvs_p": null,
"transcript": "NM_001419876.1",
"protein_id": "NP_001406805.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001419876.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "SETDB2-PHF11",
"gene_hgnc_id": null,
"hgvs_c": "c.1576+10313T>A",
"hgvs_p": null,
"transcript": "NM_001320727.2",
"protein_id": "NP_001307656.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 825,
"cds_start": null,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320727.2"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.53T>A",
"hgvs_p": null,
"transcript": "ENST00000467763.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000467763.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.24T>A",
"hgvs_p": null,
"transcript": "ENST00000476953.6",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000476953.6"
},
{
"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": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.372T>A",
"hgvs_p": null,
"transcript": "ENST00000481509.5",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000481509.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.427T>A",
"hgvs_p": null,
"transcript": "ENST00000482487.5",
"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": "ENST00000482487.5"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.84T>A",
"hgvs_p": null,
"transcript": "NR_135322.2",
"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_135322.2"
},
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.84T>A",
"hgvs_p": null,
"transcript": "NR_135323.3",
"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_135323.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SETDB2-PHF11",
"gene_hgnc_id": null,
"hgvs_c": "n.2662+5126T>A",
"hgvs_p": null,
"transcript": "NR_135324.2",
"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_135324.2"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.-200T>A",
"hgvs_p": null,
"transcript": "ENST00000487433.6",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000487433.6"
}
],
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"dbsnp": "rs893951899",
"frequency_reference_population": 0.000021773596,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.000022754,
"gnomad_genomes_af": 0.0000132256,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07310494780540466,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.128,
"revel_prediction": "Benign",
"alphamissense_score": 0.0997,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.122,
"phylop100way_prediction": "Benign",
"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": 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_001040443.3",
"gene_symbol": "PHF11",
"hgnc_id": 17024,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.35T>A",
"hgvs_p": "p.Val12Glu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001320727.2",
"gene_symbol": "SETDB2-PHF11",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1576+10313T>A",
"hgvs_p": null
}
],
"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
}