rs7715826

chr5-160066051-C-T

Variant summary

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

The XM_011534424.4(PWWP2A):c.1550-2378G>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 XM_011534424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PWWP2A	XM_011534424.4	c.1550-2378G>A		intron_variant
PWWP2A	XR_007058578.1	n.1612-2378G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PWWP2A	ENST00000524050.5	c.*236+497G>A		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0198

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0561 Hom.: 129

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7715826; hg19: chr5-159493058;