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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: X-77681710-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77681710&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "ATRX",
"hgnc_id": 886,
"hgvs_c": "c.3546G>A",
"hgvs_p": "p.Lys1182Lys",
"inheritance_mode": "XL",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_000489.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_score": -3,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "X",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Alpha thalassemia-X-linked intellectual disability syndrome",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4099999964237213,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2492,
"aa_ref": "K",
"aa_start": 1182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11165,
"cdna_start": 3761,
"cds_end": null,
"cds_length": 7479,
"cds_start": 3546,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_000489.6",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3546G>A",
"hgvs_p": "p.Lys1182Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000373344.11",
"protein_coding": true,
"protein_id": "NP_000480.3",
"strand": false,
"transcript": "NM_000489.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2492,
"aa_ref": "K",
"aa_start": 1182,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11165,
"cdna_start": 3761,
"cds_end": null,
"cds_length": 7479,
"cds_start": 3546,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000373344.11",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3546G>A",
"hgvs_p": "p.Lys1182Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000489.6",
"protein_coding": true,
"protein_id": "ENSP00000362441.4",
"strand": false,
"transcript": "ENST00000373344.11",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2454,
"aa_ref": "K",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10218,
"cdna_start": 3647,
"cds_end": null,
"cds_length": 7365,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000395603.7",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3432G>A",
"hgvs_p": "p.Lys1144Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378967.3",
"strand": false,
"transcript": "ENST00000395603.7",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1350,
"aa_ref": "K",
"aa_start": 1114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4272,
"cdna_start": 3561,
"cds_end": null,
"cds_length": 4053,
"cds_start": 3342,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000624166.3",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3342G>A",
"hgvs_p": "p.Lys1114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000485103.1",
"strand": false,
"transcript": "ENST00000624166.3",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 293,
"aa_ref": "K",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2967,
"cdna_start": 432,
"cds_end": null,
"cds_length": 882,
"cds_start": 432,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000493470.2",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.432G>A",
"hgvs_p": "p.Lys144Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000485408.1",
"strand": false,
"transcript": "ENST00000493470.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 10455,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 36,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000480283.5",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "n.*3174G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000480196.1",
"strand": false,
"transcript": "ENST00000480283.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 10455,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 36,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000480283.5",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "n.*3174G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000480196.1",
"strand": false,
"transcript": "ENST00000480283.5",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2454,
"aa_ref": "K",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11051,
"cdna_start": 3647,
"cds_end": null,
"cds_length": 7365,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_138270.5",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3432G>A",
"hgvs_p": "p.Lys1144Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_612114.2",
"strand": false,
"transcript": "NM_138270.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2491,
"aa_ref": "K",
"aa_start": 1181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11162,
"cdna_start": 3758,
"cds_end": null,
"cds_length": 7476,
"cds_start": 3543,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_005262153.6",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3543G>A",
"hgvs_p": "p.Lys1181Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262210.2",
"strand": false,
"transcript": "XM_005262153.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2463,
"aa_ref": "K",
"aa_start": 1153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11078,
"cdna_start": 3674,
"cds_end": null,
"cds_length": 7392,
"cds_start": 3459,
"consequences": [
"synonymous_variant"
],
"exon_count": 36,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005262154.6",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3459G>A",
"hgvs_p": "p.Lys1153Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262211.2",
"strand": false,
"transcript": "XM_005262154.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2462,
"aa_ref": "K",
"aa_start": 1152,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11075,
"cdna_start": 3671,
"cds_end": null,
"cds_length": 7389,
"cds_start": 3456,
"consequences": [
"synonymous_variant"
],
"exon_count": 36,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017029601.3",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3456G>A",
"hgvs_p": "p.Lys1152Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016885090.1",
"strand": false,
"transcript": "XM_017029601.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2453,
"aa_ref": "K",
"aa_start": 1143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11048,
"cdna_start": 3644,
"cds_end": null,
"cds_length": 7362,
"cds_start": 3429,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_006724666.5",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3429G>A",
"hgvs_p": "p.Lys1143Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724729.1",
"strand": false,
"transcript": "XM_006724666.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2437,
"aa_ref": "K",
"aa_start": 1127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11052,
"cdna_start": 3648,
"cds_end": null,
"cds_length": 7314,
"cds_start": 3381,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_005262156.5",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3381G>A",
"hgvs_p": "p.Lys1127Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262213.2",
"strand": false,
"transcript": "XM_005262156.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2425,
"aa_ref": "K",
"aa_start": 1115,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10964,
"cdna_start": 3560,
"cds_end": null,
"cds_length": 7278,
"cds_start": 3345,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_017029604.3",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3345G>A",
"hgvs_p": "p.Lys1115Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016885093.1",
"strand": false,
"transcript": "XM_017029604.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2424,
"aa_ref": "K",
"aa_start": 1114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10961,
"cdna_start": 3557,
"cds_end": null,
"cds_length": 7275,
"cds_start": 3342,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_005262157.6",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3342G>A",
"hgvs_p": "p.Lys1114Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262214.2",
"strand": false,
"transcript": "XM_005262157.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 2038,
"aa_ref": "K",
"aa_start": 1182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6398,
"cdna_start": 3761,
"cds_end": null,
"cds_length": 6117,
"cds_start": 3546,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047442191.1",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3546G>A",
"hgvs_p": "p.Lys1182Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298147.1",
"strand": false,
"transcript": "XM_047442191.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1871,
"aa_ref": "K",
"aa_start": 1182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6044,
"cdna_start": 3761,
"cds_end": null,
"cds_length": 5616,
"cds_start": 3546,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_006724668.4",
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"hgvs_c": "c.3546G>A",
"hgvs_p": "p.Lys1182Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006724731.1",
"strand": false,
"transcript": "XM_006724668.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1490780716",
"effect": "synonymous_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 886,
"gene_symbol": "ATRX",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Alpha thalassemia-X-linked intellectual disability syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.304,
"pos": 77681710,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000489.6"
}
]
}