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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: 19-38287937-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38287937&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 38287937,
"ref": "T",
"alt": "C",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_021102.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "NM_021102.4",
"protein_id": "NP_066925.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 252,
"cds_start": null,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000301244.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021102.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000301244.12",
"protein_id": "ENSP00000301244.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 252,
"cds_start": null,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021102.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301244.12"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.166+2T>C",
"hgvs_p": null,
"transcript": "ENST00000454580.7",
"protein_id": "ENSP00000389788.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": null,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454580.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.339T>C",
"hgvs_p": "p.Gly113Gly",
"transcript": "ENST00000918440.1",
"protein_id": "ENSP00000588499.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 251,
"cds_start": 339,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918440.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.168T>C",
"hgvs_p": "p.Gly56Gly",
"transcript": "ENST00000964703.1",
"protein_id": "ENSP00000634762.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 194,
"cds_start": 168,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964703.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000902579.1",
"protein_id": "ENSP00000572638.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 259,
"cds_start": null,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902579.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.334+5T>C",
"hgvs_p": null,
"transcript": "ENST00000918438.1",
"protein_id": "ENSP00000588497.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918438.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000918441.1",
"protein_id": "ENSP00000588500.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 241,
"cds_start": null,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918441.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000964700.1",
"protein_id": "ENSP00000634759.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 239,
"cds_start": null,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964700.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.278-2182T>C",
"hgvs_p": null,
"transcript": "ENST00000902578.1",
"protein_id": "ENSP00000572637.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 214,
"cds_start": null,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902578.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.187+2T>C",
"hgvs_p": null,
"transcript": "ENST00000587090.5",
"protein_id": "ENSP00000466407.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 202,
"cds_start": null,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587090.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000964701.1",
"protein_id": "ENSP00000634760.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": null,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964701.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.166+2T>C",
"hgvs_p": null,
"transcript": "NM_001166103.2",
"protein_id": "NP_001159575.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": null,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166103.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.163+5T>C",
"hgvs_p": null,
"transcript": "ENST00000918439.1",
"protein_id": "ENSP00000588498.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 194,
"cds_start": null,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918439.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.337+2T>C",
"hgvs_p": null,
"transcript": "ENST00000964702.1",
"protein_id": "ENSP00000634761.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": null,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964702.1"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.107-1201T>C",
"hgvs_p": null,
"transcript": "ENST00000902577.1",
"protein_id": "ENSP00000572636.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 175,
"cds_start": null,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902577.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.278-1201T>C",
"hgvs_p": null,
"transcript": "ENST00000587516.5",
"protein_id": "ENSP00000465721.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 173,
"cds_start": null,
"cds_end": null,
"cds_length": 524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587516.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "n.536T>C",
"hgvs_p": null,
"transcript": "ENST00000590210.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000590210.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.*2T>C",
"hgvs_p": null,
"transcript": "ENST00000592007.1",
"protein_id": "ENSP00000465561.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": null,
"cds_end": null,
"cds_length": 187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592007.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"hgvs_c": "c.*32T>C",
"hgvs_p": null,
"transcript": "ENST00000590510.5",
"protein_id": "ENSP00000465301.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 51,
"cds_start": null,
"cds_end": null,
"cds_length": 157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590510.5"
}
],
"gene_symbol": "SPINT2",
"gene_hgnc_id": 11247,
"dbsnp": "rs606231155",
"frequency_reference_population": 0.0000013681332,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136813,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1599999964237213,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6399999856948853,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.345,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.91,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.990945634311904,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_021102.4",
"gene_symbol": "SPINT2",
"hgnc_id": 11247,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.337+2T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital secretory sodium diarrhea 3",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital secretory sodium diarrhea 3",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}