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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: 1-230067369-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=230067369&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 230067369,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004481.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "NM_004481.5",
"protein_id": "NP_004472.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 571,
"cds_start": 89,
"cds_end": null,
"cds_length": 1716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000366672.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004481.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000366672.5",
"protein_id": "ENSP00000355632.4",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 571,
"cds_start": 89,
"cds_end": null,
"cds_length": 1716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004481.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000366672.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000935982.1",
"protein_id": "ENSP00000606041.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 579,
"cds_start": 89,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935982.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000950855.1",
"protein_id": "ENSP00000620914.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 578,
"cds_start": 89,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950855.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000868579.1",
"protein_id": "ENSP00000538638.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 570,
"cds_start": 89,
"cds_end": null,
"cds_length": 1713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868579.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000950857.1",
"protein_id": "ENSP00000620916.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 549,
"cds_start": 89,
"cds_end": null,
"cds_length": 1650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950857.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000868580.1",
"protein_id": "ENSP00000538639.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 507,
"cds_start": 89,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868580.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000935981.1",
"protein_id": "ENSP00000606040.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 501,
"cds_start": 89,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935981.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000950856.1",
"protein_id": "ENSP00000620915.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 501,
"cds_start": 89,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950856.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000935979.1",
"protein_id": "ENSP00000606038.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 494,
"cds_start": 89,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935979.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000868581.1",
"protein_id": "ENSP00000538640.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 437,
"cds_start": 89,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868581.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val",
"transcript": "ENST00000935980.1",
"protein_id": "ENSP00000606039.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 315,
"cds_start": 89,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935980.1"
},
{
"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": 16,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "c.12+9291C>T",
"hgvs_p": null,
"transcript": "NM_001291866.2",
"protein_id": "NP_001278795.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 533,
"cds_start": null,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291866.2"
},
{
"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": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "n.111C>T",
"hgvs_p": null,
"transcript": "ENST00000488903.1",
"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": "pseudogene",
"feature": "ENST00000488903.1"
},
{
"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": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "n.132C>T",
"hgvs_p": null,
"transcript": "NR_120373.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_120373.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"hgvs_c": "n.89+9291C>T",
"hgvs_p": null,
"transcript": "ENST00000494106.1",
"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": "pseudogene",
"feature": "ENST00000494106.1"
}
],
"gene_symbol": "GALNT2",
"gene_hgnc_id": 4124,
"dbsnp": "rs753282220",
"frequency_reference_population": 0.000019544083,
"hom_count_reference_population": 1,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.000020333,
"gnomad_genomes_af": 0.0000133351,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13993406295776367,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.075,
"revel_prediction": "Benign",
"alphamissense_score": 0.0971,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.382,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_004481.5",
"gene_symbol": "GALNT2",
"hgnc_id": 4124,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Ala30Val"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}