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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: 7-157549019-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=157549019&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 157549019,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001308268.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2903G>A",
"hgvs_p": "p.Gly968Asp",
"transcript": "NM_002847.5",
"protein_id": "NP_002838.2",
"transcript_support_level": null,
"aa_start": 968,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2903,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000389418.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002847.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2903G>A",
"hgvs_p": "p.Gly968Asp",
"transcript": "ENST00000389418.9",
"protein_id": "ENSP00000374069.4",
"transcript_support_level": 1,
"aa_start": 968,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2903,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002847.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389418.9"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2852G>A",
"hgvs_p": "p.Gly951Asp",
"transcript": "ENST00000389416.8",
"protein_id": "ENSP00000374067.4",
"transcript_support_level": 1,
"aa_start": 951,
"aa_end": null,
"aa_length": 998,
"cds_start": 2852,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389416.8"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2816G>A",
"hgvs_p": "p.Gly939Asp",
"transcript": "ENST00000389413.7",
"protein_id": "ENSP00000374064.3",
"transcript_support_level": 1,
"aa_start": 939,
"aa_end": null,
"aa_length": 986,
"cds_start": 2816,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389413.7"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2972G>A",
"hgvs_p": "p.Gly991Asp",
"transcript": "NM_001308268.2",
"protein_id": "NP_001295197.1",
"transcript_support_level": null,
"aa_start": 991,
"aa_end": null,
"aa_length": 1038,
"cds_start": 2972,
"cds_end": null,
"cds_length": 3117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308268.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2852G>A",
"hgvs_p": "p.Gly951Asp",
"transcript": "NM_130842.4",
"protein_id": "NP_570857.2",
"transcript_support_level": null,
"aa_start": 951,
"aa_end": null,
"aa_length": 998,
"cds_start": 2852,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130842.4"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2816G>A",
"hgvs_p": "p.Gly939Asp",
"transcript": "NM_130843.4",
"protein_id": "NP_570858.2",
"transcript_support_level": null,
"aa_start": 939,
"aa_end": null,
"aa_length": 986,
"cds_start": 2816,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130843.4"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2789G>A",
"hgvs_p": "p.Gly930Asp",
"transcript": "NM_001308267.2",
"protein_id": "NP_001295196.1",
"transcript_support_level": null,
"aa_start": 930,
"aa_end": null,
"aa_length": 977,
"cds_start": 2789,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308267.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2789G>A",
"hgvs_p": "p.Gly930Asp",
"transcript": "ENST00000409483.5",
"protein_id": "ENSP00000387114.1",
"transcript_support_level": 2,
"aa_start": 930,
"aa_end": null,
"aa_length": 977,
"cds_start": 2789,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409483.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.707G>A",
"hgvs_p": "p.Gly236Asp",
"transcript": "ENST00000648371.1",
"protein_id": "ENSP00000498058.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 293,
"cds_start": 707,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648371.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2765G>A",
"hgvs_p": "p.Gly922Asp",
"transcript": "XM_047420678.1",
"protein_id": "XP_047276634.1",
"transcript_support_level": null,
"aa_start": 922,
"aa_end": null,
"aa_length": 969,
"cds_start": 2765,
"cds_end": null,
"cds_length": 2910,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420678.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2705G>A",
"hgvs_p": "p.Gly902Asp",
"transcript": "XM_017012475.1",
"protein_id": "XP_016867964.1",
"transcript_support_level": null,
"aa_start": 902,
"aa_end": null,
"aa_length": 949,
"cds_start": 2705,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017012475.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"hgvs_c": "c.2702G>A",
"hgvs_p": "p.Gly901Asp",
"transcript": "XM_047420679.1",
"protein_id": "XP_047276635.1",
"transcript_support_level": null,
"aa_start": 901,
"aa_end": null,
"aa_length": 948,
"cds_start": 2702,
"cds_end": null,
"cds_length": 2847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420679.1"
}
],
"gene_symbol": "PTPRN2",
"gene_hgnc_id": 9677,
"dbsnp": "rs139873095",
"frequency_reference_population": 0.0000061955334,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000547251,
"gnomad_genomes_af": 0.0000131394,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8635614514350891,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8159999847412109,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.704,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9832,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.088,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999539617043849,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001308268.2",
"gene_symbol": "PTPRN2",
"hgnc_id": 9677,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2972G>A",
"hgvs_p": "p.Gly991Asp"
}
],
"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
}