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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: 2-46614938-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=46614938&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 46614938,
"ref": "T",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_002643.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "NM_002643.4",
"protein_id": "NP_002634.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 219,
"cds_start": 227,
"cds_end": null,
"cds_length": 660,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 1294,
"mane_select": "ENST00000281382.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "ENST00000281382.11",
"protein_id": "ENSP00000281382.6",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 219,
"cds_start": 227,
"cds_end": null,
"cds_length": 660,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 1294,
"mane_select": "NM_002643.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "ENST00000306465.8",
"protein_id": "ENSP00000302663.4",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 206,
"cds_start": 227,
"cds_end": null,
"cds_length": 621,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 1061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "NM_173074.3",
"protein_id": "NP_775097.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 206,
"cds_start": 227,
"cds_end": null,
"cds_length": 621,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "XM_011532908.4",
"protein_id": "XP_011531210.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 227,
"cds_start": 227,
"cds_end": null,
"cds_length": 684,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 1346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met",
"transcript": "XM_005264369.4",
"protein_id": "XP_005264426.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 187,
"cds_start": 227,
"cds_end": null,
"cds_length": 564,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 1418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "n.227A>T",
"hgvs_p": null,
"transcript": "ENST00000412717.1",
"protein_id": "ENSP00000413202.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "n.227A>T",
"hgvs_p": null,
"transcript": "ENST00000420164.6",
"protein_id": "ENSP00000410361.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "n.2093A>T",
"hgvs_p": null,
"transcript": "ENST00000495933.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"hgvs_c": "c.*80A>T",
"hgvs_p": null,
"transcript": "ENST00000474980.1",
"protein_id": "ENSP00000429355.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 48,
"cds_start": -4,
"cds_end": null,
"cds_length": 147,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PIGF",
"gene_hgnc_id": 8962,
"dbsnp": "rs541951074",
"frequency_reference_population": 0.000020196949,
"hom_count_reference_population": 0,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.0000121543,
"gnomad_genomes_af": 0.0000854038,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.855379045009613,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.6700000166893005,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.271,
"revel_prediction": "Benign",
"alphamissense_score": 0.3421,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.974,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.16,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.991408333924719,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002643.4",
"gene_symbol": "PIGF",
"hgnc_id": 8962,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.227A>T",
"hgvs_p": "p.Lys76Met"
}
],
"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
}