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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: 1-172388786-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=172388786&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 172388786,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001350204.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2499G>A",
"hgvs_p": "p.Thr833Thr",
"transcript": "NM_015569.5",
"protein_id": "NP_056384.2",
"transcript_support_level": null,
"aa_start": 833,
"aa_end": null,
"aa_length": 863,
"cds_start": 2499,
"cds_end": null,
"cds_length": 2592,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000627582.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015569.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2499G>A",
"hgvs_p": "p.Thr833Thr",
"transcript": "ENST00000627582.3",
"protein_id": "ENSP00000486701.1",
"transcript_support_level": 1,
"aa_start": 833,
"aa_end": null,
"aa_length": 863,
"cds_start": 2499,
"cds_end": null,
"cds_length": 2592,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015569.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000627582.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2487G>A",
"hgvs_p": "p.Thr829Thr",
"transcript": "ENST00000367731.5",
"protein_id": "ENSP00000356705.1",
"transcript_support_level": 1,
"aa_start": 829,
"aa_end": null,
"aa_length": 859,
"cds_start": 2487,
"cds_end": null,
"cds_length": 2580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000367731.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr",
"transcript": "ENST00000485254.3",
"protein_id": "ENSP00000429165.2",
"transcript_support_level": 1,
"aa_start": 839,
"aa_end": null,
"aa_length": 858,
"cds_start": 2517,
"cds_end": null,
"cds_length": 2577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000485254.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr",
"transcript": "NM_001350204.2",
"protein_id": "NP_001337133.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 869,
"cds_start": 2517,
"cds_end": null,
"cds_length": 2610,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350204.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr",
"transcript": "ENST00000355305.9",
"protein_id": "ENSP00000347457.5",
"transcript_support_level": 5,
"aa_start": 839,
"aa_end": null,
"aa_length": 869,
"cds_start": 2517,
"cds_end": null,
"cds_length": 2610,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355305.9"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2487G>A",
"hgvs_p": "p.Thr829Thr",
"transcript": "NM_001136127.3",
"protein_id": "NP_001129599.1",
"transcript_support_level": null,
"aa_start": 829,
"aa_end": null,
"aa_length": 859,
"cds_start": 2487,
"cds_end": null,
"cds_length": 2580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136127.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr",
"transcript": "NM_001350206.2",
"protein_id": "NP_001337135.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 858,
"cds_start": 2517,
"cds_end": null,
"cds_length": 2577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350206.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2673G>A",
"hgvs_p": "p.Thr891Thr",
"transcript": "XM_017000976.2",
"protein_id": "XP_016856465.1",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 921,
"cds_start": 2673,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000976.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2661G>A",
"hgvs_p": "p.Thr887Thr",
"transcript": "XM_017000977.2",
"protein_id": "XP_016856466.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 917,
"cds_start": 2661,
"cds_end": null,
"cds_length": 2754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000977.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2643G>A",
"hgvs_p": "p.Thr881Thr",
"transcript": "XM_017000978.2",
"protein_id": "XP_016856467.1",
"transcript_support_level": null,
"aa_start": 881,
"aa_end": null,
"aa_length": 911,
"cds_start": 2643,
"cds_end": null,
"cds_length": 2736,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000978.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2673G>A",
"hgvs_p": "p.Thr891Thr",
"transcript": "XM_017000979.2",
"protein_id": "XP_016856468.1",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 910,
"cds_start": 2673,
"cds_end": null,
"cds_length": 2733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000979.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2544G>A",
"hgvs_p": "p.Thr848Thr",
"transcript": "XM_017000980.2",
"protein_id": "XP_016856469.1",
"transcript_support_level": null,
"aa_start": 848,
"aa_end": null,
"aa_length": 878,
"cds_start": 2544,
"cds_end": null,
"cds_length": 2637,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000980.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2529G>A",
"hgvs_p": "p.Thr843Thr",
"transcript": "XM_005245079.2",
"protein_id": "XP_005245136.1",
"transcript_support_level": null,
"aa_start": 843,
"aa_end": null,
"aa_length": 873,
"cds_start": 2529,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245079.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr",
"transcript": "XM_017000982.3",
"protein_id": "XP_016856471.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 858,
"cds_start": 2517,
"cds_end": null,
"cds_length": 2577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000982.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2487G>A",
"hgvs_p": "p.Thr829Thr",
"transcript": "XM_017000984.2",
"protein_id": "XP_016856473.1",
"transcript_support_level": null,
"aa_start": 829,
"aa_end": null,
"aa_length": 848,
"cds_start": 2487,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000984.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2487G>A",
"hgvs_p": "p.Thr829Thr",
"transcript": "XM_017000985.2",
"protein_id": "XP_016856474.1",
"transcript_support_level": null,
"aa_start": 829,
"aa_end": null,
"aa_length": 848,
"cds_start": 2487,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000985.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2487G>A",
"hgvs_p": "p.Thr829Thr",
"transcript": "XM_047417389.1",
"protein_id": "XP_047273345.1",
"transcript_support_level": null,
"aa_start": 829,
"aa_end": null,
"aa_length": 846,
"cds_start": 2487,
"cds_end": null,
"cds_length": 2541,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417389.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "c.2388G>A",
"hgvs_p": "p.Thr796Thr",
"transcript": "XM_017000986.2",
"protein_id": "XP_016856475.1",
"transcript_support_level": null,
"aa_start": 796,
"aa_end": null,
"aa_length": 815,
"cds_start": 2388,
"cds_end": null,
"cds_length": 2448,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000986.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "n.386G>A",
"hgvs_p": null,
"transcript": "ENST00000491124.1",
"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": "retained_intron",
"feature": "ENST00000491124.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"hgvs_c": "n.2692G>A",
"hgvs_p": null,
"transcript": "NR_146559.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_146559.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGC",
"gene_hgnc_id": 8960,
"hgvs_c": "n.182-1829C>T",
"hgvs_p": null,
"transcript": "ENST00000475059.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000475059.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGC",
"gene_hgnc_id": 8960,
"hgvs_c": "n.132-10528C>T",
"hgvs_p": null,
"transcript": "ENST00000489002.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000489002.5"
}
],
"gene_symbol": "DNM3",
"gene_hgnc_id": 29125,
"dbsnp": "rs2301454",
"frequency_reference_population": 0.0021066128,
"hom_count_reference_population": 90,
"allele_count_reference_population": 3355,
"gnomad_exomes_af": 0.00205936,
"gnomad_genomes_af": 0.00255333,
"gnomad_exomes_ac": 2966,
"gnomad_genomes_ac": 389,
"gnomad_exomes_homalt": 80,
"gnomad_genomes_homalt": 10,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9800000190734863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.98,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.011,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001350204.2",
"gene_symbol": "DNM3",
"hgnc_id": 29125,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2517G>A",
"hgvs_p": "p.Thr839Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000475059.5",
"gene_symbol": "PIGC",
"hgnc_id": 8960,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.182-1829C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}