13-31068344-A-T

Position:

• chr13-31068344-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425638.2(WDR95P):​n.282+918A>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR95P	ENST00000425638.2	n.282+918A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.500

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7996548; hg19: chr13-31642481;