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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: 11-47438002-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=47438002&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 47438002,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_005055.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1212C>T",
"hgvs_p": "p.Arg404Arg",
"transcript": "NM_005055.5",
"protein_id": "NP_005046.2",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 412,
"cds_start": 1212,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1384,
"cdna_end": null,
"cdna_length": 1622,
"mane_select": "ENST00000298854.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1212C>T",
"hgvs_p": "p.Arg404Arg",
"transcript": "ENST00000298854.7",
"protein_id": "ENSP00000298854.2",
"transcript_support_level": 1,
"aa_start": 404,
"aa_end": null,
"aa_length": 412,
"cds_start": 1212,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1384,
"cdna_end": null,
"cdna_length": 1622,
"mane_select": "NM_005055.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1035C>T",
"hgvs_p": "p.Arg345Arg",
"transcript": "ENST00000352508.7",
"protein_id": "ENSP00000298853.3",
"transcript_support_level": 1,
"aa_start": 345,
"aa_end": null,
"aa_length": 353,
"cds_start": 1035,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1214,
"cdna_end": null,
"cdna_length": 1452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1348C>T",
"hgvs_p": "p.Leu450Phe",
"transcript": "NM_001440490.1",
"protein_id": "NP_001427419.1",
"transcript_support_level": null,
"aa_start": 450,
"aa_end": null,
"aa_length": 520,
"cds_start": 1348,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1520,
"cdna_end": null,
"cdna_length": 1758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Leu433Phe",
"transcript": "NM_001440491.1",
"protein_id": "NP_001427420.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 503,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1469,
"cdna_end": null,
"cdna_length": 1707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1015C>T",
"hgvs_p": "p.Leu339Phe",
"transcript": "NM_001440493.1",
"protein_id": "NP_001427422.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 409,
"cds_start": 1015,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 1187,
"cdna_end": null,
"cdna_length": 1425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1012C>T",
"hgvs_p": "p.Leu338Phe",
"transcript": "NM_001440494.1",
"protein_id": "NP_001427423.1",
"transcript_support_level": null,
"aa_start": 338,
"aa_end": null,
"aa_length": 408,
"cds_start": 1012,
"cds_end": null,
"cds_length": 1227,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 1422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.958C>T",
"hgvs_p": "p.Leu320Phe",
"transcript": "NM_001440496.1",
"protein_id": "NP_001427425.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 390,
"cds_start": 958,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 1368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.835C>T",
"hgvs_p": "p.Leu279Phe",
"transcript": "NM_001440501.1",
"protein_id": "NP_001427430.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 349,
"cds_start": 835,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 1007,
"cdna_end": null,
"cdna_length": 1245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1158C>T",
"hgvs_p": "p.Arg386Arg",
"transcript": "NM_001440495.1",
"protein_id": "NP_001427424.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 394,
"cds_start": 1158,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 1330,
"cdna_end": null,
"cdna_length": 1568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1089C>T",
"hgvs_p": "p.Arg363Arg",
"transcript": "NM_001440497.1",
"protein_id": "NP_001427426.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 371,
"cds_start": 1089,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 1261,
"cdna_end": null,
"cdna_length": 1499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1053C>T",
"hgvs_p": "p.Arg351Arg",
"transcript": "NM_001440499.1",
"protein_id": "NP_001427428.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 359,
"cds_start": 1053,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1225,
"cdna_end": null,
"cdna_length": 1463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1053C>T",
"hgvs_p": "p.Arg351Arg",
"transcript": "ENST00000524487.5",
"protein_id": "ENSP00000435551.2",
"transcript_support_level": 5,
"aa_start": 351,
"aa_end": null,
"aa_length": 359,
"cds_start": 1053,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1225,
"cdna_end": null,
"cdna_length": 1462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.1035C>T",
"hgvs_p": "p.Arg345Arg",
"transcript": "NM_032645.5",
"protein_id": "NP_116034.2",
"transcript_support_level": null,
"aa_start": 345,
"aa_end": null,
"aa_length": 353,
"cds_start": 1035,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1207,
"cdna_end": null,
"cdna_length": 1445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.999C>T",
"hgvs_p": "p.Arg333Arg",
"transcript": "NM_001440502.1",
"protein_id": "NP_001427431.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 341,
"cds_start": 999,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 1409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.930C>T",
"hgvs_p": "p.Arg310Arg",
"transcript": "NM_001440503.1",
"protein_id": "NP_001427432.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 318,
"cds_start": 930,
"cds_end": null,
"cds_length": 957,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 1340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.873C>T",
"hgvs_p": "p.Arg291Arg",
"transcript": "NM_001440504.1",
"protein_id": "NP_001427433.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 299,
"cds_start": 873,
"cds_end": null,
"cds_length": 900,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 1283,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "n.167C>T",
"hgvs_p": null,
"transcript": "ENST00000528356.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.*657C>T",
"hgvs_p": null,
"transcript": "NM_001440492.1",
"protein_id": "NP_001427421.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.*657C>T",
"hgvs_p": null,
"transcript": "NM_001440498.1",
"protein_id": "NP_001427427.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": -4,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"hgvs_c": "c.*657C>T",
"hgvs_p": null,
"transcript": "NM_001440500.1",
"protein_id": "NP_001427429.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 353,
"cds_start": -4,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124902673",
"gene_hgnc_id": null,
"hgvs_c": "n.144+235G>A",
"hgvs_p": null,
"transcript": "XR_007062669.1",
"protein_id": null,
"transcript_support_level": null,
"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": 255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAPSN",
"gene_hgnc_id": 9863,
"dbsnp": "rs2076326463",
"frequency_reference_population": 0.000001934982,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 7.15197e-7,
"gnomad_genomes_af": 0.0000131418,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2370000034570694,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.237,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.037,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4,BP6,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_005055.5",
"gene_symbol": "RAPSN",
"hgnc_id": 9863,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1212C>T",
"hgvs_p": "p.Arg404Arg"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007062669.1",
"gene_symbol": "LOC124902673",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.144+235G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital myasthenic syndrome 11,Fetal akinesia deformation sequence 1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Congenital myasthenic syndrome 11|Fetal akinesia deformation sequence 1|Congenital myasthenic syndrome 11;Fetal akinesia deformation sequence 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}