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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: 1-160130436-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=160130436&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"PM1",
"PP2",
"BP4_Strong",
"BP6",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP1A2",
"hgnc_id": 800,
"hgvs_c": "c.1666A>T",
"hgvs_p": "p.Asn556Tyr",
"inheritance_mode": "AD,AR",
"pathogenic_score": 3,
"score": -6,
"transcript": "NM_000702.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP2,BP4_Strong,BP6,BS1",
"acmg_score": -6,
"allele_count_reference_population": 423,
"alphamissense_prediction": null,
"alphamissense_score": 0.0907,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 2, familial hemiplegic,Alternating hemiplegia of childhood 1,Familial hemiplegic migraine,Migraine,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:3 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.03818318247795105,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1020,
"aa_ref": "N",
"aa_start": 556,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5435,
"cdna_start": 1769,
"cds_end": null,
"cds_length": 3063,
"cds_start": 1666,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_000702.4",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1666A>T",
"hgvs_p": "p.Asn556Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000361216.8",
"protein_coding": true,
"protein_id": "NP_000693.1",
"strand": true,
"transcript": "NM_000702.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1020,
"aa_ref": "N",
"aa_start": 556,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5435,
"cdna_start": 1769,
"cds_end": null,
"cds_length": 3063,
"cds_start": 1666,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000361216.8",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1666A>T",
"hgvs_p": "p.Asn556Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000702.4",
"protein_coding": true,
"protein_id": "ENSP00000354490.3",
"strand": true,
"transcript": "ENST00000361216.8",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1028,
"aa_ref": "N",
"aa_start": 564,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4682,
"cdna_start": 1789,
"cds_end": null,
"cds_length": 3087,
"cds_start": 1690,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000857225.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1690A>T",
"hgvs_p": "p.Asn564Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527284.1",
"strand": true,
"transcript": "ENST00000857225.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1019,
"aa_ref": "N",
"aa_start": 556,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5433,
"cdna_start": 1770,
"cds_end": null,
"cds_length": 3060,
"cds_start": 1666,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000969831.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1666A>T",
"hgvs_p": "p.Asn556Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639890.1",
"strand": true,
"transcript": "ENST00000969831.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1017,
"aa_ref": "N",
"aa_start": 553,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5415,
"cdna_start": 1760,
"cds_end": null,
"cds_length": 3054,
"cds_start": 1657,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000969832.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1657A>T",
"hgvs_p": "p.Asn553Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639891.1",
"strand": true,
"transcript": "ENST00000969832.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1010,
"aa_ref": "N",
"aa_start": 546,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5405,
"cdna_start": 1735,
"cds_end": null,
"cds_length": 3033,
"cds_start": 1636,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000857224.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1636A>T",
"hgvs_p": "p.Asn546Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527283.1",
"strand": true,
"transcript": "ENST00000857224.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1009,
"aa_ref": "N",
"aa_start": 556,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3338,
"cdna_start": 1751,
"cds_end": null,
"cds_length": 3030,
"cds_start": 1666,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000392233.7",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1666A>T",
"hgvs_p": "p.Asn556Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376066.3",
"strand": true,
"transcript": "ENST00000392233.7",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 999,
"aa_ref": "N",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5372,
"cdna_start": 1702,
"cds_end": null,
"cds_length": 3000,
"cds_start": 1603,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000857223.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1603A>T",
"hgvs_p": "p.Asn535Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527282.1",
"strand": true,
"transcript": "ENST00000857223.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 952,
"aa_ref": "N",
"aa_start": 488,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4283,
"cdna_start": 1566,
"cds_end": null,
"cds_length": 2859,
"cds_start": 1462,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000969833.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.1462A>T",
"hgvs_p": "p.Asn488Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639892.1",
"strand": true,
"transcript": "ENST00000969833.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 713,
"aa_ref": "N",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4413,
"cdna_start": 798,
"cds_end": null,
"cds_length": 2142,
"cds_start": 796,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000447527.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.796A>T",
"hgvs_p": "p.Asn266Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000411705.1",
"strand": true,
"transcript": "ENST00000447527.1",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 723,
"aa_ref": "N",
"aa_start": 259,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4451,
"cdna_start": 785,
"cds_end": null,
"cds_length": 2172,
"cds_start": 775,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047421286.1",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "c.775A>T",
"hgvs_p": "p.Asn259Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047277242.1",
"strand": true,
"transcript": "XM_047421286.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000472488.5",
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"hgvs_c": "n.1769A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000472488.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs141467566",
"effect": "missense_variant",
"frequency_reference_population": 0.00026207464,
"gene_hgnc_id": 800,
"gene_symbol": "ATP1A2",
"gnomad_exomes_ac": 396,
"gnomad_exomes_af": 0.000270882,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 27,
"gnomad_genomes_af": 0.000177454,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Migraine, familial hemiplegic, 2|Familial hemiplegic migraine|not specified|Alternating hemiplegia of childhood 1|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.025,
"pos": 160130436,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.217,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000702.4"
}
]
}