13-31068344-A-T

Variant names:

• chr13-31068344-A-T
• rs7996548
• ENST00000425638.2:n.282+918A>T

Variant summary

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

The ENST00000425638.2(WDR95P):​n.282+918A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,064 control chromosomes in the GnomAD database, including 19,474 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 0.47 (19474 hom., cov: 32)
• Consequence: WDR95P ENST00000425638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

WDR95P (HGNC:42637): (WD repeat domain 95, pseudogene)

ENSG00000304093 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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
WDR95P	ENST00000425638.2	n.282+918A>T		intron_variant	Intron 3 of 15	6
ENSG00000304093	ENST00000799653.1	n.353-8504A>T		intron_variant	Intron 4 of 4
ENSG00000304222	ENST00000801137.1	n.127-3964T>A		intron_variant	Intron 1 of 1
ENSG00000304222	ENST00000801138.1	n.127-3968T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71155 AN: 151946 Hom.: 19467 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.468 AC: 71179 AN: 152064 Hom.: 19474 Cov.: 32 AF XY: 0.478 AC XY: 35495 AN XY: 74330

African (AFR) AF: 0.173 AC: 7190 AN: 41498

American (AMR) AF: 0.608 AC: 9290 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4195 AN: 5168

South Asian (SAS) AF: 0.662 AC: 3182 AN: 4808

European-Finnish (FIN) AF: 0.629 AC: 6658 AN: 10582

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37137 AN: 67958

Other (OTH) AF: 0.500 AC: 1055 AN: 2108

Alfa AF: 0.341 Hom.: 938

Bravo AF: 0.457

Asia WGS AF: 0.689 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7996548; hg19: chr13-31642481;