← 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: 2-86604558-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86604558&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 86604558,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005667.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1343A>G",
"hgvs_p": "p.Asn448Ser",
"transcript": "NM_005667.4",
"protein_id": "NP_005658.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 685,
"cds_start": 1343,
"cds_end": null,
"cds_length": 2058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000237455.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005667.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1343A>G",
"hgvs_p": "p.Asn448Ser",
"transcript": "ENST00000237455.5",
"protein_id": "ENSP00000237455.4",
"transcript_support_level": 1,
"aa_start": 448,
"aa_end": null,
"aa_length": 685,
"cds_start": 1343,
"cds_end": null,
"cds_length": 2058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005667.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237455.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.132+15772A>G",
"hgvs_p": null,
"transcript": "ENST00000604011.5",
"protein_id": "ENSP00000474823.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000604011.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.357+195T>C",
"hgvs_p": null,
"transcript": "ENST00000426549.1",
"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": "pseudogene",
"feature": "ENST00000426549.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1415A>G",
"hgvs_p": "p.Asn472Ser",
"transcript": "ENST00000886122.1",
"protein_id": "ENSP00000556181.1",
"transcript_support_level": null,
"aa_start": 472,
"aa_end": null,
"aa_length": 709,
"cds_start": 1415,
"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": "ENST00000886122.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1358A>G",
"hgvs_p": "p.Asn453Ser",
"transcript": "ENST00000886123.1",
"protein_id": "ENSP00000556182.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 690,
"cds_start": 1358,
"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": "ENST00000886123.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1334A>G",
"hgvs_p": "p.Asn445Ser",
"transcript": "ENST00000949491.1",
"protein_id": "ENSP00000619550.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 682,
"cds_start": 1334,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949491.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1331A>G",
"hgvs_p": "p.Asn444Ser",
"transcript": "NM_001198951.1",
"protein_id": "NP_001185880.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 681,
"cds_start": 1331,
"cds_end": null,
"cds_length": 2046,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198951.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.367-80A>G",
"hgvs_p": null,
"transcript": "ENST00000949492.1",
"protein_id": "ENSP00000619551.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 333,
"cds_start": null,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949492.1"
},
{
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.132+15772A>G",
"hgvs_p": null,
"transcript": "NM_001198954.1",
"protein_id": "NP_001185883.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198954.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.366+15772A>G",
"hgvs_p": null,
"transcript": "ENST00000440757.2",
"protein_id": "ENSP00000392995.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": null,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440757.2"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "n.3402A>G",
"hgvs_p": null,
"transcript": "ENST00000472030.1",
"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": "ENST00000472030.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.74+195T>C",
"hgvs_p": null,
"transcript": "ENST00000424788.1",
"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": "ENST00000424788.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.249-12618T>C",
"hgvs_p": null,
"transcript": "ENST00000439077.1",
"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": "ENST00000439077.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "n.528-80A>G",
"hgvs_p": null,
"transcript": "ENST00000463333.6",
"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": "ENST00000463333.6"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.645-12618T>C",
"hgvs_p": null,
"transcript": "ENST00000597638.1",
"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": "ENST00000597638.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.223-12618T>C",
"hgvs_p": null,
"transcript": "ENST00000725269.1",
"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": "ENST00000725269.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.259+195T>C",
"hgvs_p": null,
"transcript": "ENST00000725270.1",
"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": "ENST00000725270.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.254-12618T>C",
"hgvs_p": null,
"transcript": "NR_183900.1",
"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_183900.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.645-12618T>C",
"hgvs_p": null,
"transcript": "NR_183901.1",
"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_183901.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "n.*42A>G",
"hgvs_p": null,
"transcript": "ENST00000477307.5",
"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": "pseudogene",
"feature": "ENST00000477307.5"
}
],
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"dbsnp": "rs1486313743",
"frequency_reference_population": 0.000010531494,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.00000889267,
"gnomad_genomes_af": 0.0000262591,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2019193172454834,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.132,
"revel_prediction": "Benign",
"alphamissense_score": 0.1103,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.61,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005667.4",
"gene_symbol": "RNF103",
"hgnc_id": 12859,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1343A>G",
"hgvs_p": "p.Asn448Ser"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001198954.1",
"gene_symbol": "RNF103-CHMP3",
"hgnc_id": 38847,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.132+15772A>G",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000426549.1",
"gene_symbol": "CHMP3-AS1",
"hgnc_id": 55795,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.357+195T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}