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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: 16-1592176-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1592176&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1592176,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000426508.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "NM_014714.4",
"protein_id": "NP_055529.2",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 5232,
"mane_select": "ENST00000426508.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "ENST00000426508.7",
"protein_id": "ENSP00000406012.2",
"transcript_support_level": 5,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 5232,
"mane_select": "NM_014714.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_006720990.4",
"protein_id": "XP_006721053.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 950,
"cdna_end": null,
"cdna_length": 5222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_006720991.4",
"protein_id": "XP_006721054.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 6238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434965.1",
"protein_id": "XP_047290921.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 703,
"cdna_end": null,
"cdna_length": 4975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434966.1",
"protein_id": "XP_047290922.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 1516,
"cdna_end": null,
"cdna_length": 5788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434967.1",
"protein_id": "XP_047290923.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 2092,
"cdna_end": null,
"cdna_length": 6364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434968.1",
"protein_id": "XP_047290924.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 2103,
"cdna_end": null,
"cdna_length": 6375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434969.1",
"protein_id": "XP_047290925.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1462,
"cds_start": 634,
"cds_end": null,
"cds_length": 4389,
"cdna_start": 1419,
"cdna_end": null,
"cdna_length": 5691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434970.1",
"protein_id": "XP_047290926.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 1380,
"cds_start": 634,
"cds_end": null,
"cds_length": 4143,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 4986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_011522769.4",
"protein_id": "XP_011521071.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 817,
"cds_start": 634,
"cds_end": null,
"cds_length": 2454,
"cdna_start": 960,
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"cdna_length": 3598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434972.1",
"protein_id": "XP_047290928.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 811,
"cds_start": 634,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 960,
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"cdna_length": 5824,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_005255725.6",
"protein_id": "XP_005255782.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 807,
"cds_start": 634,
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"cdna_start": 960,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
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"intron_rank": null,
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"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434973.1",
"protein_id": "XP_047290929.1",
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"cds_start": 634,
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"cdna_start": 1966,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_011522771.4",
"protein_id": "XP_011521073.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 806,
"cds_start": 634,
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"cdna_start": 960,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
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"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434974.1",
"protein_id": "XP_047290930.1",
"transcript_support_level": null,
"aa_start": 212,
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"aa_length": 806,
"cds_start": 634,
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"cdna_start": 1966,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434975.1",
"protein_id": "XP_047290931.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 806,
"cds_start": 634,
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"cdna_start": 950,
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"cdna_length": 3866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_011522772.4",
"protein_id": "XP_011521074.1",
"transcript_support_level": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
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"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434976.1",
"protein_id": "XP_047290932.1",
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_005255726.5",
"protein_id": "XP_005255783.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434977.1",
"protein_id": "XP_047290933.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 801,
"cds_start": 634,
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"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT140",
"gene_hgnc_id": 29077,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg",
"transcript": "XM_047434978.1",
"protein_id": "XP_047290934.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 801,
"cds_start": 634,
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"cdna_start": 950,
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"mane_select": null,
"mane_plus": null,
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{
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{
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"hgvs_c": "n.329-7756G>A",
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"transcript": "ENST00000397417.6",
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{
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"exon_count": 3,
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{
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],
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"exon_count": 3,
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"gene_symbol": "LOC105371046",
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}
],
"gene_symbol": "IFT140",
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"dbsnp": "rs201188361",
"frequency_reference_population": 0.000103468104,
"hom_count_reference_population": 0,
"allele_count_reference_population": 167,
"gnomad_exomes_af": 0.000104664,
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"gnomad_exomes_ac": 153,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9144041538238525,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9660000205039978,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.463,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5526,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.14,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.608,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.61,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999986590681012,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000426508.7",
"gene_symbol": "IFT140",
"hgnc_id": 29077,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Gly212Arg"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000563162.1",
"gene_symbol": "ENSG00000260989",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.59+11591C>T",
"hgvs_p": null
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_135176.1",
"gene_symbol": "LOC105371046",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.59+11591C>T",
"hgvs_p": null
}
],
"clinvar_disease": "IFT140-related disorder,Jeune thoracic dystrophy,Nephronophthisis,Retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene,Retinitis pigmentosa 80,Saldino-Mainzer syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:1",
"phenotype_combined": "Saldino-Mainzer syndrome|not provided|Jeune thoracic dystrophy|Retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene|Retinitis pigmentosa 80;Saldino-Mainzer syndrome|Nephronophthisis|IFT140-related disorder|Retinitis pigmentosa 80",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}