5-160092772-C-T

Variant names:

• chr5-160092772-C-T
• rs1271271347
• NM_001130864.2:c.1878G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130864.2(PWWP2A):​c.1878G>A​(p.Glu626Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000286 in 1,399,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: PWWP2A NM_001130864.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.79
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130864.2. 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
	PWWP2A	NM_001130864.2	MANE Select	c.1878G>A	p.Glu626Glu	synonymous	Exon 2 of 2	NP_001124336.1	Q96N64-1
	PWWP2A	NM_001349732.2		c.1227G>A	p.Glu409Glu	synonymous	Exon 4 of 4	NP_001336661.1
	PWWP2A	NM_052927.4		c.1549+329G>A		intron	N/A	NP_443159.1	Q96N64-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWWP2A	ENST00000307063.9	TSL:1 MANE Select	c.1878G>A	p.Glu626Glu	synonymous	Exon 2 of 2	ENSP00000305151.7	Q96N64-1
	PWWP2A	ENST00000456329.7	TSL:1	c.1549+329G>A		intron	N/A	ENSP00000390462.2	Q96N64-2
	PWWP2A	ENST00000523662.1	TSL:1	c.1549+329G>A		intron	N/A	ENSP00000428143.1	Q96N64-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000286 AC: 4 AN: 1399340 Hom.: 0 Cov.: 32 AF XY: 0.00000580 AC XY: 4 AN XY: 690180

African (AFR) AF: 0.00 AC: 0 AN: 31592

American (AMR) AF: 0.00 AC: 0 AN: 35682

Ashkenazi Jewish (ASJ) AF: 0.0000397 AC: 1 AN: 25180

East Asian (EAS) AF: 0.00 AC: 0 AN: 35738

South Asian (SAS) AF: 0.00 AC: 0 AN: 79236

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49274

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5698

European-Non Finnish (NFE) AF: 0.00000278 AC: 3 AN: 1078946

Other (OTH) AF: 0.00 AC: 0 AN: 57994

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	8.3
DANN	Benign	0.48
PhyloP100		5.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1271271347; hg19: chr5-159519779;