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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: 19-736037-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=736037&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PALM",
"hgnc_id": 8594,
"hgvs_c": "c.461C>T",
"hgvs_p": "p.Thr154Met",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_002579.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 54,
"alphamissense_prediction": null,
"alphamissense_score": 0.0844,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "atypical cerebral palsy,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.23417457938194275,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 387,
"aa_ref": "T",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2891,
"cdna_start": 673,
"cds_end": null,
"cds_length": 1164,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_002579.3",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.461C>T",
"hgvs_p": "p.Thr154Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000338448.10",
"protein_coding": true,
"protein_id": "NP_002570.2",
"strand": true,
"transcript": "NM_002579.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 387,
"aa_ref": "T",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2891,
"cdna_start": 673,
"cds_end": null,
"cds_length": 1164,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000338448.10",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.461C>T",
"hgvs_p": "p.Thr154Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002579.3",
"protein_coding": true,
"protein_id": "ENSP00000341911.4",
"strand": true,
"transcript": "ENST00000338448.10",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 343,
"aa_ref": "T",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2759,
"cdna_start": 673,
"cds_end": null,
"cds_length": 1032,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001040134.2",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.461C>T",
"hgvs_p": "p.Thr154Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001035224.1",
"strand": true,
"transcript": "NM_001040134.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 343,
"aa_ref": "T",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2755,
"cdna_start": 669,
"cds_end": null,
"cds_length": 1032,
"cds_start": 461,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000264560.11",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.461C>T",
"hgvs_p": "p.Thr154Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000264560.7",
"strand": true,
"transcript": "ENST00000264560.11",
"transcript_support_level": 4
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 336,
"aa_ref": "T",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2551,
"cdna_start": 466,
"cds_end": null,
"cds_length": 1011,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000964891.1",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.440C>T",
"hgvs_p": "p.Thr147Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634950.1",
"strand": true,
"transcript": "ENST00000964891.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 242,
"aa_ref": "T",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2272,
"cdna_start": 54,
"cds_end": null,
"cds_length": 729,
"cds_start": 26,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000592155.5",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.26C>T",
"hgvs_p": "p.Thr9Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477952.1",
"strand": true,
"transcript": "ENST00000592155.5",
"transcript_support_level": 4
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 198,
"aa_ref": "T",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2137,
"cdna_start": 51,
"cds_end": null,
"cds_length": 597,
"cds_start": 26,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000590161.2",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.26C>T",
"hgvs_p": "p.Thr9Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480594.1",
"strand": true,
"transcript": "ENST00000590161.2",
"transcript_support_level": 4
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 389,
"aa_ref": "T",
"aa_start": 156,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2889,
"cdna_start": 671,
"cds_end": null,
"cds_length": 1170,
"cds_start": 467,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005259565.5",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.467C>T",
"hgvs_p": "p.Thr156Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259622.1",
"strand": true,
"transcript": "XM_005259565.5",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 386,
"aa_ref": "T",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3056,
"cdna_start": 838,
"cds_end": null,
"cds_length": 1161,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005259566.5",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.458C>T",
"hgvs_p": "p.Thr153Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259623.1",
"strand": true,
"transcript": "XM_005259566.5",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 345,
"aa_ref": "T",
"aa_start": 156,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2779,
"cdna_start": 693,
"cds_end": null,
"cds_length": 1038,
"cds_start": 467,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017026850.3",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "c.467C>T",
"hgvs_p": "p.Thr156Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882339.1",
"strand": true,
"transcript": "XM_017026850.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2290,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000587513.3",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "n.75C>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": "ENST00000587513.3",
"transcript_support_level": 4
},
{
"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": 579,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000589012.5",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "n.477C>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": "ENST00000589012.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2489,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000593172.5",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "n.271C>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": "ENST00000593172.5",
"transcript_support_level": 2
},
{
"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": 879,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000633534.1",
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"hgvs_c": "n.195C>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": "ENST00000633534.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs772962279",
"effect": "missense_variant",
"frequency_reference_population": 0.000033532917,
"gene_hgnc_id": 8594,
"gene_symbol": "PALM",
"gnomad_exomes_ac": 48,
"gnomad_exomes_af": 0.0000329165,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.000039442,
"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": "Uncertain significance",
"phenotype_combined": "atypical cerebral palsy|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.405,
"pos": 736037,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.067,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002579.3"
}
]
}