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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: 3-57260016-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57260016&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 57260016,
"ref": "T",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_012096.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*",
"transcript": "NM_012096.3",
"protein_id": "NP_036228.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 709,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000288266.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012096.3"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*",
"transcript": "ENST00000288266.8",
"protein_id": "ENSP00000288266.3",
"transcript_support_level": 1,
"aa_start": 552,
"aa_end": null,
"aa_length": 709,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012096.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000288266.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.1750T>A",
"hgvs_p": null,
"transcript": "ENST00000482800.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000482800.5"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*",
"transcript": "ENST00000855520.1",
"protein_id": "ENSP00000525579.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 709,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2130,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855520.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1649T>A",
"hgvs_p": "p.Leu550*",
"transcript": "ENST00000924302.1",
"protein_id": "ENSP00000594361.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 707,
"cds_start": 1649,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924302.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1613T>A",
"hgvs_p": "p.Leu538*",
"transcript": "ENST00000946520.1",
"protein_id": "ENSP00000616579.1",
"transcript_support_level": null,
"aa_start": 538,
"aa_end": null,
"aa_length": 695,
"cds_start": 1613,
"cds_end": null,
"cds_length": 2088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946520.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*",
"transcript": "ENST00000855522.1",
"protein_id": "ENSP00000525581.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 692,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2079,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855522.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1598T>A",
"hgvs_p": "p.Leu533*",
"transcript": "ENST00000855525.1",
"protein_id": "ENSP00000525584.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 690,
"cds_start": 1598,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855525.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*",
"transcript": "ENST00000946518.1",
"protein_id": "ENSP00000616577.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 679,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2040,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946518.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1508T>A",
"hgvs_p": "p.Leu503*",
"transcript": "ENST00000855524.1",
"protein_id": "ENSP00000525583.1",
"transcript_support_level": null,
"aa_start": 503,
"aa_end": null,
"aa_length": 660,
"cds_start": 1508,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855524.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1496T>A",
"hgvs_p": "p.Leu499*",
"transcript": "ENST00000855521.1",
"protein_id": "ENSP00000525580.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 656,
"cds_start": 1496,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855521.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1496T>A",
"hgvs_p": "p.Leu499*",
"transcript": "ENST00000855523.1",
"protein_id": "ENSP00000525582.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 656,
"cds_start": 1496,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855523.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1466T>A",
"hgvs_p": "p.Leu489*",
"transcript": "ENST00000946519.1",
"protein_id": "ENSP00000616578.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 646,
"cds_start": 1466,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946519.1"
},
{
"aa_ref": "L",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "c.1604T>A",
"hgvs_p": "p.Leu535*",
"transcript": "XM_011533583.4",
"protein_id": "XP_011531885.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 692,
"cds_start": 1604,
"cds_end": null,
"cds_length": 2079,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533583.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.560T>A",
"hgvs_p": null,
"transcript": "ENST00000464446.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000464446.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.490T>A",
"hgvs_p": null,
"transcript": "ENST00000488530.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000488530.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.224T>A",
"hgvs_p": null,
"transcript": "ENST00000492501.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000492501.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.1655T>A",
"hgvs_p": null,
"transcript": "ENST00000650354.1",
"protein_id": "ENSP00000498115.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000650354.1"
}
],
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"dbsnp": "rs869320673",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.626,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_012096.3",
"gene_symbol": "APPL1",
"hgnc_id": 24035,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.1655T>A",
"hgvs_p": "p.Leu552*"
}
],
"clinvar_disease": "Maturity-onset diabetes of the young type 14",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Maturity-onset diabetes of the young type 14",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}