chr13-112333875-A-G

Variant names:

• chr13-112333875-A-G
• rs9635133
• ENST00000732759.1:n.287-1156T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000732759.1(ENSG00000295796):​n.287-1156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,074 control chromosomes in the GnomAD database, including 10,526 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (10526 hom., cov: 33)
• Consequence: ENSG00000295796 ENST00000732759.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 2 publications found

Genes affected

ENSG00000295796 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295796	ENST00000732759.1	n.287-1156T>C		intron_variant	Intron 2 of 2
ENSG00000295796	ENST00000732766.1	n.-221T>C		upstream_gene_variant
ENSG00000295796	ENST00000732767.1	n.-244T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56577 AN: 151956 Hom.: 10518 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.385

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.372 AC: 56613 AN: 152074 Hom.: 10526 Cov.: 33 AF XY: 0.369 AC XY: 27399 AN XY: 74330

African (AFR) AF: 0.343 AC: 14219 AN: 41498

American (AMR) AF: 0.375 AC: 5735 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1929 AN: 5156

South Asian (SAS) AF: 0.339 AC: 1630 AN: 4808

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10576

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27073 AN: 67960

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.375 Hom.: 1331

Bravo AF: 0.378

Asia WGS AF: 0.392 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9635133; hg19: chr13-112988189;