← Back to variant description
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: 7-101215100-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=101215100&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 101215100,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001084.5",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "NM_001084.5",
"protein_id": "NP_001075.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 738,
"cds_start": 668,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 2821,
"mane_select": "ENST00000223127.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001084.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000223127.8",
"protein_id": "ENSP00000223127.3",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 738,
"cds_start": 668,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 975,
"cdna_end": null,
"cdna_length": 2821,
"mane_select": "NM_001084.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000223127.8"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890272.1",
"protein_id": "ENSP00000560331.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 762,
"cds_start": 668,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 2920,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890272.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890269.1",
"protein_id": "ENSP00000560328.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 738,
"cds_start": 668,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 2779,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890269.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890270.1",
"protein_id": "ENSP00000560329.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 738,
"cds_start": 668,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 2910,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890270.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890271.1",
"protein_id": "ENSP00000560330.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 738,
"cds_start": 668,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 2770,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890271.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890275.1",
"protein_id": "ENSP00000560334.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 729,
"cds_start": 668,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890275.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890276.1",
"protein_id": "ENSP00000560335.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 719,
"cds_start": 668,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 2783,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890276.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser",
"transcript": "ENST00000890274.1",
"protein_id": "ENSP00000560333.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 718,
"cds_start": 668,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 993,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890274.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.164A>G",
"hgvs_p": "p.Asn55Ser",
"transcript": "ENST00000421736.1",
"protein_id": "ENSP00000407908.1",
"transcript_support_level": 5,
"aa_start": 55,
"aa_end": null,
"aa_length": 268,
"cds_start": 164,
"cds_end": null,
"cds_length": 807,
"cdna_start": 166,
"cdna_end": null,
"cdna_length": 809,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421736.1"
},
{
"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": 17,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.615+808A>G",
"hgvs_p": null,
"transcript": "ENST00000890273.1",
"protein_id": "ENSP00000560332.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 684,
"cds_start": null,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2683,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890273.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "n.*55A>G",
"hgvs_p": null,
"transcript": "ENST00000424135.5",
"protein_id": "ENSP00000404799.1",
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000424135.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "n.705A>G",
"hgvs_p": null,
"transcript": "ENST00000478082.5",
"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": 1585,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000478082.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "n.*55A>G",
"hgvs_p": null,
"transcript": "ENST00000424135.5",
"protein_id": "ENSP00000404799.1",
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000424135.5"
}
],
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"dbsnp": "rs121434414",
"frequency_reference_population": 0.000017363178,
"hom_count_reference_population": 0,
"allele_count_reference_population": 28,
"gnomad_exomes_af": 0.000017804,
"gnomad_genomes_af": 0.0000131349,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9508903622627258,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.439,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3383,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.09,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001084.5",
"gene_symbol": "PLOD3",
"hgnc_id": 9083,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.668A>G",
"hgvs_p": "p.Asn223Ser"
}
],
"clinvar_disease": " and deafness, arterial rupture,Bone fragility with contractures,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Bone fragility with contractures, arterial rupture, and deafness|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}