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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: 3-156548982-ATCCT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=156548982&ref=ATCCT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 156548982,
"ref": "ATCCT",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "NM_001308197.2",
"consequences": [
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "NM_007107.5",
"protein_id": "NP_009038.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 185,
"cds_start": 278,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265044.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007107.5"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000265044.7",
"protein_id": "ENSP00000265044.2",
"transcript_support_level": 1,
"aa_start": 93,
"aa_end": null,
"aa_length": 185,
"cds_start": 278,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007107.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265044.7"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "NM_001308197.2",
"protein_id": "NP_001295126.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 198,
"cds_start": 278,
"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": "NM_001308197.2"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000467789.5",
"protein_id": "ENSP00000420641.1",
"transcript_support_level": 2,
"aa_start": 93,
"aa_end": null,
"aa_length": 198,
"cds_start": 278,
"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": "ENST00000467789.5"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000896021.1",
"protein_id": "ENSP00000566080.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 191,
"cds_start": 278,
"cds_end": null,
"cds_length": 576,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896021.1"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000896020.1",
"protein_id": "ENSP00000566079.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 185,
"cds_start": 278,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896020.1"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000960095.1",
"protein_id": "ENSP00000630154.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 178,
"cds_start": 278,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960095.1"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs",
"transcript": "ENST00000476217.5",
"protein_id": "ENSP00000417530.1",
"transcript_support_level": 3,
"aa_start": 93,
"aa_end": null,
"aa_length": 174,
"cds_start": 278,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000476217.5"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.122_125delAGGA",
"hgvs_p": "p.Glu41fs",
"transcript": "NM_001308204.2",
"protein_id": "NP_001295133.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 133,
"cds_start": 122,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308204.2"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.122_125delAGGA",
"hgvs_p": "p.Glu41fs",
"transcript": "NM_001308205.2",
"protein_id": "NP_001295134.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 133,
"cds_start": 122,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308205.2"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.122_125delAGGA",
"hgvs_p": "p.Glu41fs",
"transcript": "ENST00000463503.5",
"protein_id": "ENSP00000417306.1",
"transcript_support_level": 4,
"aa_start": 41,
"aa_end": null,
"aa_length": 133,
"cds_start": 122,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000463503.5"
},
{
"aa_ref": "ED",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.122_125delAGGA",
"hgvs_p": "p.Glu41fs",
"transcript": "ENST00000496050.1",
"protein_id": "ENSP00000420087.1",
"transcript_support_level": 4,
"aa_start": 41,
"aa_end": null,
"aa_length": 133,
"cds_start": 122,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000496050.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "c.261-4547_261-4544delAGGA",
"hgvs_p": null,
"transcript": "ENST00000926887.1",
"protein_id": "ENSP00000596946.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 152,
"cds_start": null,
"cds_end": null,
"cds_length": 459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926887.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "n.12_15delAGGA",
"hgvs_p": null,
"transcript": "ENST00000464138.1",
"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": "pseudogene",
"feature": "ENST00000464138.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "n.306_309delAGGA",
"hgvs_p": null,
"transcript": "ENST00000467733.1",
"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": "ENST00000467733.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "n.137_140delAGGA",
"hgvs_p": null,
"transcript": "ENST00000478842.5",
"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": "pseudogene",
"feature": "ENST00000478842.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"hgvs_c": "n.114_117delAGGA",
"hgvs_p": null,
"transcript": "ENST00000498205.5",
"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": "ENST00000498205.5"
}
],
"gene_symbol": "SSR3",
"gene_hgnc_id": 11325,
"dbsnp": "rs1719856599",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.842,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001308197.2",
"gene_symbol": "SSR3",
"hgnc_id": 11325,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.278_281delAGGA",
"hgvs_p": "p.Glu93fs"
}
],
"clinvar_disease": "Congenital disorder of glycosylation",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}