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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: 1-160136370-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=160136370&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 160136370,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000702.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Gly855Arg",
"transcript": "NM_000702.4",
"protein_id": "NP_000693.1",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 1020,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361216.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000702.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Gly855Arg",
"transcript": "ENST00000361216.8",
"protein_id": "ENSP00000354490.3",
"transcript_support_level": 1,
"aa_start": 855,
"aa_end": null,
"aa_length": 1020,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000702.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361216.8"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2587G>A",
"hgvs_p": "p.Gly863Arg",
"transcript": "ENST00000857225.1",
"protein_id": "ENSP00000527284.1",
"transcript_support_level": null,
"aa_start": 863,
"aa_end": null,
"aa_length": 1028,
"cds_start": 2587,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857225.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Gly855Arg",
"transcript": "ENST00000969831.1",
"protein_id": "ENSP00000639890.1",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 1019,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3060,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969831.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2554G>A",
"hgvs_p": "p.Gly852Arg",
"transcript": "ENST00000969832.1",
"protein_id": "ENSP00000639891.1",
"transcript_support_level": null,
"aa_start": 852,
"aa_end": null,
"aa_length": 1017,
"cds_start": 2554,
"cds_end": null,
"cds_length": 3054,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969832.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2533G>A",
"hgvs_p": "p.Gly845Arg",
"transcript": "ENST00000857224.1",
"protein_id": "ENSP00000527283.1",
"transcript_support_level": null,
"aa_start": 845,
"aa_end": null,
"aa_length": 1010,
"cds_start": 2533,
"cds_end": null,
"cds_length": 3033,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857224.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Gly855Arg",
"transcript": "ENST00000392233.7",
"protein_id": "ENSP00000376066.3",
"transcript_support_level": 5,
"aa_start": 855,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2563,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392233.7"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2500G>A",
"hgvs_p": "p.Gly834Arg",
"transcript": "ENST00000857223.1",
"protein_id": "ENSP00000527282.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 999,
"cds_start": 2500,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857223.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.2359G>A",
"hgvs_p": "p.Gly787Arg",
"transcript": "ENST00000969833.1",
"protein_id": "ENSP00000639892.1",
"transcript_support_level": null,
"aa_start": 787,
"aa_end": null,
"aa_length": 952,
"cds_start": 2359,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969833.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1693G>A",
"hgvs_p": "p.Glu565Lys",
"transcript": "ENST00000447527.1",
"protein_id": "ENSP00000411705.1",
"transcript_support_level": 2,
"aa_start": 565,
"aa_end": null,
"aa_length": 713,
"cds_start": 1693,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447527.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1672G>A",
"hgvs_p": "p.Gly558Arg",
"transcript": "XM_047421286.1",
"protein_id": "XP_047277242.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 723,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2172,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421286.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "n.2666G>A",
"hgvs_p": null,
"transcript": "ENST00000472488.5",
"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": "ENST00000472488.5"
}
],
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"dbsnp": "rs1553245857",
"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": 0.9882763028144836,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.958,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9993,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.031,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.48,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.99999742736349,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000702.4",
"gene_symbol": "ATP1A2",
"hgnc_id": 800,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2563G>A",
"hgvs_p": "p.Gly855Arg"
}
],
"clinvar_disease": " 2, and dysmorphic facies, familial hemiplegic, microcephaly, polymicrogyria, respiratory insufficiency,Alternating hemiplegia of childhood 1,Developmental and epileptic encephalopathy 98,Familial hemiplegic migraine,Fetal akinesia,Migraine,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "Familial hemiplegic migraine|not provided|Migraine, familial hemiplegic, 2;Alternating hemiplegia of childhood 1|Migraine, familial hemiplegic, 2;Alternating hemiplegia of childhood 1;Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies;Developmental and epileptic encephalopathy 98",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}