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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: 2-197398499-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=197398499&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 197398499,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_012433.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.3096A>G",
"hgvs_p": "p.Gln1032Gln",
"transcript": "NM_012433.4",
"protein_id": "NP_036565.2",
"transcript_support_level": null,
"aa_start": 1032,
"aa_end": null,
"aa_length": 1304,
"cds_start": 3096,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 3125,
"cdna_end": null,
"cdna_length": 6463,
"mane_select": "ENST00000335508.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012433.4"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.3096A>G",
"hgvs_p": "p.Gln1032Gln",
"transcript": "ENST00000335508.11",
"protein_id": "ENSP00000335321.6",
"transcript_support_level": 1,
"aa_start": 1032,
"aa_end": null,
"aa_length": 1304,
"cds_start": 3096,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 3125,
"cdna_end": null,
"cdna_length": 6463,
"mane_select": "NM_012433.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335508.11"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.3093A>G",
"hgvs_p": "p.Gln1031Gln",
"transcript": "ENST00000929354.1",
"protein_id": "ENSP00000599413.1",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1303,
"cds_start": 3093,
"cds_end": null,
"cds_length": 3912,
"cdna_start": 3123,
"cdna_end": null,
"cdna_length": 4410,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929354.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.3015A>G",
"hgvs_p": "p.Gln1005Gln",
"transcript": "ENST00000929356.1",
"protein_id": "ENSP00000599415.1",
"transcript_support_level": null,
"aa_start": 1005,
"aa_end": null,
"aa_length": 1277,
"cds_start": 3015,
"cds_end": null,
"cds_length": 3834,
"cdna_start": 3042,
"cdna_end": null,
"cdna_length": 4180,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929356.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.3096A>G",
"hgvs_p": "p.Gln1032Gln",
"transcript": "ENST00000929355.1",
"protein_id": "ENSP00000599414.1",
"transcript_support_level": null,
"aa_start": 1032,
"aa_end": null,
"aa_length": 1260,
"cds_start": 3096,
"cds_end": null,
"cds_length": 3783,
"cdna_start": 3122,
"cdna_end": null,
"cdna_length": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929355.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2925A>G",
"hgvs_p": "p.Gln975Gln",
"transcript": "ENST00000963258.1",
"protein_id": "ENSP00000633317.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1247,
"cds_start": 2925,
"cds_end": null,
"cds_length": 3744,
"cdna_start": 2974,
"cdna_end": null,
"cdna_length": 4121,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963258.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2730A>G",
"hgvs_p": "p.Gln910Gln",
"transcript": "ENST00000963259.1",
"protein_id": "ENSP00000633318.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 1182,
"cds_start": 2730,
"cds_end": null,
"cds_length": 3549,
"cdna_start": 2776,
"cdna_end": null,
"cdna_length": 3911,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963259.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2223A>G",
"hgvs_p": "p.Gln741Gln",
"transcript": "ENST00000963257.1",
"protein_id": "ENSP00000633316.1",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2223,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 2261,
"cdna_end": null,
"cdna_length": 3475,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963257.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.141A>G",
"hgvs_p": "p.Gln47Gln",
"transcript": "ENST00000424674.1",
"protein_id": "ENSP00000409435.1",
"transcript_support_level": 4,
"aa_start": 47,
"aa_end": null,
"aa_length": 239,
"cds_start": 141,
"cds_end": null,
"cds_length": 721,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 723,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424674.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2658A>G",
"hgvs_p": "p.Gln886Gln",
"transcript": "XM_047443838.1",
"protein_id": "XP_047299794.1",
"transcript_support_level": null,
"aa_start": 886,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2658,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 4390,
"cdna_end": null,
"cdna_length": 7728,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443838.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2658A>G",
"hgvs_p": "p.Gln886Gln",
"transcript": "XM_047443839.1",
"protein_id": "XP_047299795.1",
"transcript_support_level": null,
"aa_start": 886,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2658,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 4106,
"cdna_end": null,
"cdna_length": 7444,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443839.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.4980A>G",
"hgvs_p": null,
"transcript": "ENST00000470268.2",
"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": 8308,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000470268.2"
},
{
"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": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.274A>G",
"hgvs_p": null,
"transcript": "ENST00000496458.1",
"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": 475,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000496458.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*4163A>G",
"hgvs_p": null,
"transcript": "ENST00000652026.1",
"protein_id": "ENSP00000498652.1",
"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": 9283,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000652026.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*3355A>G",
"hgvs_p": null,
"transcript": "ENST00000652738.1",
"protein_id": "ENSP00000499119.1",
"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": 8478,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000652738.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*4163A>G",
"hgvs_p": null,
"transcript": "ENST00000652026.1",
"protein_id": "ENSP00000498652.1",
"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": 9283,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000652026.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*3355A>G",
"hgvs_p": null,
"transcript": "ENST00000652738.1",
"protein_id": "ENSP00000499119.1",
"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": 8478,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000652738.1"
},
{
"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": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.*73A>G",
"hgvs_p": null,
"transcript": "XM_047443840.1",
"protein_id": "XP_047299796.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": null,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3248,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443840.1"
}
],
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"dbsnp": "rs34532346",
"frequency_reference_population": 0.00057750026,
"hom_count_reference_population": 0,
"allele_count_reference_population": 932,
"gnomad_exomes_af": 0.000589784,
"gnomad_genomes_af": 0.000459619,
"gnomad_exomes_ac": 862,
"gnomad_genomes_ac": 70,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.032999999821186066,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.033,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.2,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_012433.4",
"gene_symbol": "SF3B1",
"hgnc_id": 10768,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3096A>G",
"hgvs_p": "p.Gln1032Gln"
}
],
"clinvar_disease": "SF3B1-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SF3B1-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}