rs7715826

Variant names:

• chr5-160066051-C-T
• rs7715826
• ENST00000524050.5:n.*236+497G>A

Variant summary

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

The ENST00000524050.5(PWWP2A):​n.*236+497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 152,198 control chromosomes in the GnomAD database, including 455 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 0.070 (455 hom., cov: 32)
• Consequence: PWWP2A ENST00000524050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 3 publications found

Genes affected

PWWP2A (HGNC:29406): (PWWP domain containing 2A) Enables chromatin binding activity and histone binding activity. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PWWP2A	XM_011534424.4	c.1550-2378G>A		intron_variant	Intron 2 of 3		XP_011532726.1
PWWP2A	XR_007058578.1	n.1612-2378G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PWWP2A	ENST00000524050.5	n.*236+497G>A		intron_variant	Intron 4 of 5	3		ENSP00000428636.1

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 10603 AN: 152080 Hom.: 448 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0725

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

GnomAD4 genome AF: 0.0699 AC: 10642 AN: 152198 Hom.: 455 Cov.: 32 AF XY: 0.0683 AC XY: 5087 AN XY: 74426

African (AFR) AF: 0.119 AC: 4955 AN: 41506

American (AMR) AF: 0.0564 AC: 862 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3468

East Asian (EAS) AF: 0.102 AC: 528 AN: 5178

South Asian (SAS) AF: 0.0917 AC: 442 AN: 4822

European-Finnish (FIN) AF: 0.0198 AC: 210 AN: 10608

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3254 AN: 68024

Other (OTH) AF: 0.0769 AC: 162 AN: 2106

Alfa AF: 0.0566 Hom.: 147

Bravo AF: 0.0749

Asia WGS AF: 0.103 AC: 358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.53
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs7715826; hg19: chr5-159493058;