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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: 2-127654505-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=127654505&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 127654505,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000355119.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.278A>G",
"hgvs_p": "p.Asn93Ser",
"transcript": "NM_001161403.3",
"protein_id": "NP_001154875.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 341,
"cds_start": 278,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": "ENST00000355119.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.278A>G",
"hgvs_p": "p.Asn93Ser",
"transcript": "ENST00000355119.9",
"protein_id": "ENSP00000347240.4",
"transcript_support_level": 1,
"aa_start": 93,
"aa_end": null,
"aa_length": 341,
"cds_start": 278,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 2387,
"mane_select": "NM_001161403.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.350A>G",
"hgvs_p": "p.Asn117Ser",
"transcript": "ENST00000324938.9",
"protein_id": "ENSP00000326888.5",
"transcript_support_level": 1,
"aa_start": 117,
"aa_end": null,
"aa_length": 365,
"cds_start": 350,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 2111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Asn88Ser",
"transcript": "ENST00000409455.5",
"protein_id": "ENSP00000386383.1",
"transcript_support_level": 1,
"aa_start": 88,
"aa_end": null,
"aa_length": 336,
"cds_start": 263,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 899,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Asn88Ser",
"transcript": "ENST00000410011.5",
"protein_id": "ENSP00000387002.1",
"transcript_support_level": 1,
"aa_start": 88,
"aa_end": null,
"aa_length": 336,
"cds_start": 263,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 734,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.350A>G",
"hgvs_p": "p.Asn117Ser",
"transcript": "NM_017980.5",
"protein_id": "NP_060450.2",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 365,
"cds_start": 350,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 2158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.344A>G",
"hgvs_p": "p.Asn115Ser",
"transcript": "NM_001136037.4",
"protein_id": "NP_001129509.2",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 363,
"cds_start": 344,
"cds_end": null,
"cds_length": 1092,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.344A>G",
"hgvs_p": "p.Asn115Ser",
"transcript": "ENST00000545738.6",
"protein_id": "ENSP00000443794.2",
"transcript_support_level": 5,
"aa_start": 115,
"aa_end": null,
"aa_length": 363,
"cds_start": 344,
"cds_end": null,
"cds_length": 1092,
"cdna_start": 422,
"cdna_end": null,
"cdna_length": 1730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Asn88Ser",
"transcript": "NM_001161404.2",
"protein_id": "NP_001154876.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 336,
"cds_start": 263,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 734,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Asn88Ser",
"transcript": "ENST00000409808.6",
"protein_id": "ENSP00000386637.2",
"transcript_support_level": 5,
"aa_start": 88,
"aa_end": null,
"aa_length": 336,
"cds_start": 263,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.335A>G",
"hgvs_p": "p.Asn112Ser",
"transcript": "XM_047444963.1",
"protein_id": "XP_047300919.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 360,
"cds_start": 335,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 522,
"cdna_end": null,
"cdna_length": 2125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Asn88Ser",
"transcript": "XM_024452983.2",
"protein_id": "XP_024308751.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 336,
"cds_start": 263,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.350A>G",
"hgvs_p": "p.Asn117Ser",
"transcript": "XM_011511453.2",
"protein_id": "XP_011509755.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 324,
"cds_start": 350,
"cds_end": null,
"cds_length": 975,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 2035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.278A>G",
"hgvs_p": "p.Asn93Ser",
"transcript": "XM_047444970.1",
"protein_id": "XP_047300926.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 300,
"cds_start": 278,
"cds_end": null,
"cds_length": 903,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 2264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.350A>G",
"hgvs_p": "p.Asn117Ser",
"transcript": "XM_047444971.1",
"protein_id": "XP_047300927.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 277,
"cds_start": 350,
"cds_end": null,
"cds_length": 834,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 1091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.71A>G",
"hgvs_p": "p.Asn24Ser",
"transcript": "XM_005263710.3",
"protein_id": "XP_005263767.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 272,
"cds_start": 71,
"cds_end": null,
"cds_length": 819,
"cdna_start": 624,
"cdna_end": null,
"cdna_length": 2227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.350A>G",
"hgvs_p": "p.Asn117Ser",
"transcript": "XM_006712628.4",
"protein_id": "XP_006712691.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 190,
"cds_start": 350,
"cds_end": null,
"cds_length": 573,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.414A>G",
"hgvs_p": null,
"transcript": "ENST00000466410.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.1296A>G",
"hgvs_p": null,
"transcript": "ENST00000469300.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "n.666A>G",
"hgvs_p": null,
"transcript": "ENST00000476932.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"hgvs_c": "c.12-11433A>G",
"hgvs_p": null,
"transcript": "XM_006712627.5",
"protein_id": "XP_006712690.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 225,
"cds_start": -4,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LIMS2",
"gene_hgnc_id": 16084,
"dbsnp": "rs373800371",
"frequency_reference_population": 0.00025154333,
"hom_count_reference_population": 0,
"allele_count_reference_population": 406,
"gnomad_exomes_af": 0.000264055,
"gnomad_genomes_af": 0.000131387,
"gnomad_exomes_ac": 386,
"gnomad_genomes_ac": 20,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1849096417427063,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.242,
"revel_prediction": "Benign",
"alphamissense_score": 0.0547,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.356,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000355119.9",
"gene_symbol": "LIMS2",
"hgnc_id": 16084,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.278A>G",
"hgvs_p": "p.Asn93Ser"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2W,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2W|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}