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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: 4-151102889-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=151102889&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 151102889,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001006.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Val125Ile",
"transcript": "NM_001006.5",
"protein_id": "NP_000997.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 264,
"cds_start": 373,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000274065.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001006.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Val125Ile",
"transcript": "ENST00000274065.9",
"protein_id": "ENSP00000346050.3",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 264,
"cds_start": 373,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001006.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274065.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "n.210G>A",
"hgvs_p": null,
"transcript": "ENST00000507485.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000507485.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Val125Ile",
"transcript": "ENST00000913221.1",
"protein_id": "ENSP00000583280.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 260,
"cds_start": 373,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913221.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Val88Ile",
"transcript": "ENST00000506126.5",
"protein_id": "ENSP00000426282.1",
"transcript_support_level": 5,
"aa_start": 88,
"aa_end": null,
"aa_length": 227,
"cds_start": 262,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506126.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Val88Ile",
"transcript": "ENST00000514682.5",
"protein_id": "ENSP00000421770.1",
"transcript_support_level": 5,
"aa_start": 88,
"aa_end": null,
"aa_length": 227,
"cds_start": 262,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514682.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.313G>A",
"hgvs_p": "p.Val105Ile",
"transcript": "ENST00000510993.1",
"protein_id": "ENSP00000426466.1",
"transcript_support_level": 5,
"aa_start": 105,
"aa_end": null,
"aa_length": 222,
"cds_start": 313,
"cds_end": null,
"cds_length": 670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510993.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.205G>A",
"hgvs_p": "p.Val69Ile",
"transcript": "ENST00000515792.5",
"protein_id": "ENSP00000425508.1",
"transcript_support_level": 3,
"aa_start": 69,
"aa_end": null,
"aa_length": 208,
"cds_start": 205,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515792.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Val125Ile",
"transcript": "ENST00000512690.5",
"protein_id": "ENSP00000423953.1",
"transcript_support_level": 3,
"aa_start": 125,
"aa_end": null,
"aa_length": 205,
"cds_start": 373,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512690.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Val88Ile",
"transcript": "ENST00000507327.5",
"protein_id": "ENSP00000424547.1",
"transcript_support_level": 2,
"aa_start": 88,
"aa_end": null,
"aa_length": 192,
"cds_start": 262,
"cds_end": null,
"cds_length": 581,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507327.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Val120Ile",
"transcript": "ENST00000512797.5",
"protein_id": "ENSP00000421457.1",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 190,
"cds_start": 358,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512797.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.16G>A",
"hgvs_p": "p.Val6Ile",
"transcript": "ENST00000509736.5",
"protein_id": "ENSP00000422994.1",
"transcript_support_level": 2,
"aa_start": 6,
"aa_end": null,
"aa_length": 145,
"cds_start": 16,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509736.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Val88Ile",
"transcript": "ENST00000508783.5",
"protein_id": "ENSP00000421776.1",
"transcript_support_level": 3,
"aa_start": 88,
"aa_end": null,
"aa_length": 124,
"cds_start": 262,
"cds_end": null,
"cds_length": 377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508783.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.262G>A",
"hgvs_p": "p.Val88Ile",
"transcript": "ENST00000505243.5",
"protein_id": "ENSP00000425024.1",
"transcript_support_level": 3,
"aa_start": 88,
"aa_end": null,
"aa_length": 100,
"cds_start": 262,
"cds_end": null,
"cds_length": 305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505243.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.*8G>A",
"hgvs_p": null,
"transcript": "NM_001267699.2",
"protein_id": "NP_001254628.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": null,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001267699.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.355-75G>A",
"hgvs_p": null,
"transcript": "ENST00000913223.1",
"protein_id": "ENSP00000583282.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 233,
"cds_start": null,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913223.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.355-99G>A",
"hgvs_p": null,
"transcript": "ENST00000913224.1",
"protein_id": "ENSP00000583283.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 225,
"cds_start": null,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913224.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.355-159G>A",
"hgvs_p": null,
"transcript": "ENST00000913225.1",
"protein_id": "ENSP00000583284.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 205,
"cds_start": null,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913225.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.205-99G>A",
"hgvs_p": null,
"transcript": "ENST00000913222.1",
"protein_id": "ENSP00000583281.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 175,
"cds_start": null,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913222.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "c.63-1288G>A",
"hgvs_p": null,
"transcript": "ENST00000968783.1",
"protein_id": "ENSP00000638842.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 97,
"cds_start": null,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968783.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "n.*8G>A",
"hgvs_p": null,
"transcript": "ENST00000515818.5",
"protein_id": "ENSP00000425978.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000515818.5"
},
{
"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": "SH3D19",
"gene_hgnc_id": 30418,
"hgvs_c": "n.365C>T",
"hgvs_p": null,
"transcript": "ENST00000604922.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000604922.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"hgvs_c": "n.*8G>A",
"hgvs_p": null,
"transcript": "ENST00000515818.5",
"protein_id": "ENSP00000425978.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000515818.5"
}
],
"gene_symbol": "RPS3A",
"gene_hgnc_id": 10421,
"dbsnp": "rs373671463",
"frequency_reference_population": 0.00011854092,
"hom_count_reference_population": 0,
"allele_count_reference_population": 191,
"gnomad_exomes_af": 0.000113082,
"gnomad_genomes_af": 0.000170893,
"gnomad_exomes_ac": 165,
"gnomad_genomes_ac": 26,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.023203939199447632,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.318,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1543,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.964,
"phylop100way_prediction": "Pathogenic",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001006.5",
"gene_symbol": "RPS3A",
"hgnc_id": 10421,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.373G>A",
"hgvs_p": "p.Val125Ile"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000604922.1",
"gene_symbol": "SH3D19",
"hgnc_id": 30418,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.365C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}