XM_011534424.4:c.1550-2378G>A

Variant names:

• chr5-160066051-C-T
• rs7715826
• XM_011534424.4:c.1550-2378G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524050.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWWP2A	ENST00000524050.5	TSL:3	n.*236+497G>A		intron	N/A	ENSP00000428636.1	H0YB44

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 v4.9

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;