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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: 21-46256907-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=46256907&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 46256907,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003906.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "NM_003906.5",
"protein_id": "NP_003897.2",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000291688.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003906.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "ENST00000291688.6",
"protein_id": "ENSP00000291688.1",
"transcript_support_level": 1,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003906.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000291688.6"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "n.407G>A",
"hgvs_p": null,
"transcript": "ENST00000467026.5",
"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": "ENST00000467026.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "ENST00000397708.1",
"protein_id": "ENSP00000380820.1",
"transcript_support_level": 5,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397708.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "XM_005261203.5",
"protein_id": "XP_005261260.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261203.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "XM_005261204.6",
"protein_id": "XP_005261261.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261204.6"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met",
"transcript": "XM_005261205.5",
"protein_id": "XP_005261262.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1980,
"cds_start": 3814,
"cds_end": null,
"cds_length": 5943,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261205.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "n.80G>A",
"hgvs_p": null,
"transcript": "ENST00000481113.1",
"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": "ENST00000481113.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "n.2106G>A",
"hgvs_p": null,
"transcript": "ENST00000486937.5",
"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": "ENST00000486937.5"
},
{
"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": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "n.238G>A",
"hgvs_p": null,
"transcript": "ENST00000494755.1",
"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": "retained_intron",
"feature": "ENST00000494755.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"hgvs_c": "n.1811G>A",
"hgvs_p": null,
"transcript": "ENST00000496607.5",
"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": "ENST00000496607.5"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.238-2017C>T",
"hgvs_p": null,
"transcript": "ENST00000590829.6",
"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": "ENST00000590829.6"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.233+15888C>T",
"hgvs_p": null,
"transcript": "ENST00000748152.1",
"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": "ENST00000748152.1"
},
{
"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": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.234+15888C>T",
"hgvs_p": null,
"transcript": "ENST00000748153.1",
"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": "ENST00000748153.1"
},
{
"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": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.300+15888C>T",
"hgvs_p": null,
"transcript": "ENST00000748154.1",
"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": "ENST00000748154.1"
},
{
"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": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.293-2017C>T",
"hgvs_p": null,
"transcript": "ENST00000748155.1",
"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": "ENST00000748155.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MCM3AP-AS1",
"gene_hgnc_id": 16417,
"hgvs_c": "n.383-2017C>T",
"hgvs_p": null,
"transcript": "ENST00000748156.1",
"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": "ENST00000748156.1"
}
],
"gene_symbol": "MCM3AP",
"gene_hgnc_id": 6946,
"dbsnp": "rs779248881",
"frequency_reference_population": 0.00019940539,
"hom_count_reference_population": 0,
"allele_count_reference_population": 321,
"gnomad_exomes_af": 0.000183874,
"gnomad_genomes_af": 0.000348066,
"gnomad_exomes_ac": 268,
"gnomad_genomes_ac": 53,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004172921180725098,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.082,
"revel_prediction": "Benign",
"alphamissense_score": 0.0821,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.727,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP5,BP4",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003906.5",
"gene_symbol": "MCM3AP",
"hgnc_id": 6946,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3814G>A",
"hgvs_p": "p.Val1272Met"
},
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000590829.6",
"gene_symbol": "MCM3AP-AS1",
"hgnc_id": 16417,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.238-2017C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, with or without impaired intellectual development,Peripheral neuropathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:1 US:1",
"phenotype_combined": "Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development|not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}