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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: 17-4819581-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4819581&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 4819581,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_002663.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Gly821Ser",
"transcript": "NM_002663.5",
"protein_id": "NP_002654.3",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 933,
"cds_start": 2461,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2536,
"cdna_end": null,
"cdna_length": 3443,
"mane_select": "ENST00000263088.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002663.5"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Gly821Ser",
"transcript": "ENST00000263088.11",
"protein_id": "ENSP00000263088.5",
"transcript_support_level": 1,
"aa_start": 821,
"aa_end": null,
"aa_length": 933,
"cds_start": 2461,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2536,
"cdna_end": null,
"cdna_length": 3443,
"mane_select": "NM_002663.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263088.11"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2429+32G>A",
"hgvs_p": null,
"transcript": "ENST00000572940.5",
"protein_id": "ENSP00000459571.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": null,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3391,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000572940.5"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2518G>A",
"hgvs_p": "p.Gly840Ser",
"transcript": "ENST00000964340.1",
"protein_id": "ENSP00000634399.1",
"transcript_support_level": null,
"aa_start": 840,
"aa_end": null,
"aa_length": 952,
"cds_start": 2518,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 2628,
"cdna_end": null,
"cdna_length": 3535,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964340.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2458G>A",
"hgvs_p": "p.Gly820Ser",
"transcript": "ENST00000928900.1",
"protein_id": "ENSP00000598959.1",
"transcript_support_level": null,
"aa_start": 820,
"aa_end": null,
"aa_length": 932,
"cds_start": 2458,
"cds_end": null,
"cds_length": 2799,
"cdna_start": 2498,
"cdna_end": null,
"cdna_length": 3405,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928900.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2425G>A",
"hgvs_p": "p.Gly809Ser",
"transcript": "ENST00000879130.1",
"protein_id": "ENSP00000549189.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 921,
"cds_start": 2425,
"cds_end": null,
"cds_length": 2766,
"cdna_start": 2466,
"cdna_end": null,
"cdna_length": 3371,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879130.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2416G>A",
"hgvs_p": "p.Gly806Ser",
"transcript": "ENST00000879131.1",
"protein_id": "ENSP00000549190.1",
"transcript_support_level": null,
"aa_start": 806,
"aa_end": null,
"aa_length": 918,
"cds_start": 2416,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 2457,
"cdna_end": null,
"cdna_length": 3362,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879131.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.352G>A",
"hgvs_p": "p.Gly118Ser",
"transcript": "ENST00000576864.1",
"protein_id": "ENSP00000460477.1",
"transcript_support_level": 3,
"aa_start": 118,
"aa_end": null,
"aa_length": 196,
"cds_start": 352,
"cds_end": null,
"cds_length": 591,
"cdna_start": 353,
"cdna_end": null,
"cdna_length": 726,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000576864.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2101G>A",
"hgvs_p": "p.Gly701Ser",
"transcript": "XM_047436300.1",
"protein_id": "XP_047292256.1",
"transcript_support_level": null,
"aa_start": 701,
"aa_end": null,
"aa_length": 813,
"cds_start": 2101,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 2291,
"cdna_end": null,
"cdna_length": 3198,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436300.1"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2429+32G>A",
"hgvs_p": null,
"transcript": "NM_001243108.2",
"protein_id": "NP_001230037.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": null,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3410,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001243108.2"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2429+32G>A",
"hgvs_p": null,
"transcript": "ENST00000879132.1",
"protein_id": "ENSP00000549191.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": null,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3601,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879132.1"
},
{
"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": 24,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2429+32G>A",
"hgvs_p": null,
"transcript": "ENST00000879133.1",
"protein_id": "ENSP00000549192.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 922,
"cds_start": null,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3621,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879133.1"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.2414+47G>A",
"hgvs_p": null,
"transcript": "ENST00000964341.1",
"protein_id": "ENSP00000634400.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 917,
"cds_start": null,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3366,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964341.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "c.*66G>A",
"hgvs_p": null,
"transcript": "ENST00000576983.5",
"protein_id": "ENSP00000460250.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": null,
"cds_end": null,
"cds_length": 589,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 589,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000576983.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"hgvs_c": "n.*116G>A",
"hgvs_p": null,
"transcript": "ENST00000572127.1",
"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": 632,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000572127.1"
}
],
"gene_symbol": "PLD2",
"gene_hgnc_id": 9068,
"dbsnp": "rs3764897",
"frequency_reference_population": 0.16091573,
"hom_count_reference_population": 21543,
"allele_count_reference_population": 258375,
"gnomad_exomes_af": 0.158065,
"gnomad_genomes_af": 0.188167,
"gnomad_exomes_ac": 229759,
"gnomad_genomes_ac": 28616,
"gnomad_exomes_homalt": 18636,
"gnomad_genomes_homalt": 2907,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0037055015563964844,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.165,
"revel_prediction": "Benign",
"alphamissense_score": 0.0612,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.116,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000102425725834919,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002663.5",
"gene_symbol": "PLD2",
"hgnc_id": 9068,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Gly821Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}