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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: 17-4808301-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=4808301&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLD2",
"hgnc_id": 9068,
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_002663.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 43,
"alphamissense_prediction": null,
"alphamissense_score": 0.1089,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.4883783459663391,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 933,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3443,
"cdna_start": 343,
"cds_end": null,
"cds_length": 2802,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_002663.5",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263088.11",
"protein_coding": true,
"protein_id": "NP_002654.3",
"strand": true,
"transcript": "NM_002663.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 933,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3443,
"cdna_start": 343,
"cds_end": null,
"cds_length": 2802,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000263088.11",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002663.5",
"protein_coding": true,
"protein_id": "ENSP00000263088.5",
"strand": true,
"transcript": "ENST00000263088.11",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 922,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3391,
"cdna_start": 326,
"cds_end": null,
"cds_length": 2769,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000572940.5",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000459571.1",
"strand": true,
"transcript": "ENST00000572940.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 813,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3198,
"cdna_start": null,
"cds_end": null,
"cds_length": 2442,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047436300.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.-93C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292256.1",
"strand": true,
"transcript": "XM_047436300.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 952,
"aa_ref": "R",
"aa_start": 109,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3535,
"cdna_start": 435,
"cds_end": null,
"cds_length": 2859,
"cds_start": 325,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000964340.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634399.1",
"strand": true,
"transcript": "ENST00000964340.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 932,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3405,
"cdna_start": 308,
"cds_end": null,
"cds_length": 2799,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000928900.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000598959.1",
"strand": true,
"transcript": "ENST00000928900.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 922,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3410,
"cdna_start": 343,
"cds_end": null,
"cds_length": 2769,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001243108.2",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001230037.1",
"strand": true,
"transcript": "NM_001243108.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 922,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3601,
"cdna_start": 533,
"cds_end": null,
"cds_length": 2769,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000879132.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549191.1",
"strand": true,
"transcript": "ENST00000879132.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 922,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3621,
"cdna_start": 556,
"cds_end": null,
"cds_length": 2769,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000879133.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549192.1",
"strand": true,
"transcript": "ENST00000879133.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 921,
"aa_ref": "R",
"aa_start": 78,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3371,
"cdna_start": 273,
"cds_end": null,
"cds_length": 2766,
"cds_start": 232,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000879130.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549189.1",
"strand": true,
"transcript": "ENST00000879130.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 918,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3362,
"cdna_start": 309,
"cds_end": null,
"cds_length": 2757,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000879131.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549190.1",
"strand": true,
"transcript": "ENST00000879131.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 917,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3366,
"cdna_start": 314,
"cds_end": null,
"cds_length": 2754,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000964341.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634400.1",
"strand": true,
"transcript": "ENST00000964341.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 171,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 544,
"cdna_start": 295,
"cds_end": null,
"cds_length": 517,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000575316.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000458795.1",
"strand": true,
"transcript": "ENST00000575316.1",
"transcript_support_level": 4
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 637,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2127,
"cdna_start": 343,
"cds_end": null,
"cds_length": 1914,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047436301.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292257.1",
"strand": true,
"transcript": "XM_047436301.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 497,
"aa_ref": "R",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1616,
"cdna_start": 343,
"cds_end": null,
"cds_length": 1494,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047436302.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292258.1",
"strand": true,
"transcript": "XM_047436302.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 813,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3198,
"cdna_start": null,
"cds_end": null,
"cds_length": 2442,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047436300.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "c.-93C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292256.1",
"strand": true,
"transcript": "XM_047436300.1",
"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": 596,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000574268.1",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "n.462C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000574268.1",
"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": 2278,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000575246.6",
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"hgvs_c": "n.268C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000459304.1",
"strand": true,
"transcript": "ENST00000575246.6",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs540125550",
"effect": "missense_variant",
"frequency_reference_population": 0.000026642543,
"gene_hgnc_id": 9068,
"gene_symbol": "PLD2",
"gnomad_exomes_ac": 38,
"gnomad_exomes_af": 0.0000259951,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328627,
"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": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.079,
"pos": 4808301,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.229,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_002663.5"
}
]
}