chr19-1374642-G-A

Position:

• chr19-1374642-G-A

Variant summary

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

The NM_001369789.1(PWWP3A):​c.2075+1482G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 152,248 control chromosomes in the GnomAD database, including 541 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 0.072 (541 hom., cov: 31)
• Consequence: PWWP3A NM_001369789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

PWWP3A (HGNC:29641): (PWWP domain containing 3A, DNA repair factor) Enables nucleosome binding activity. Involved in DNA repair and chromatin organization. Located in cytosol and nucleoplasm. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PWWP3A	NM_001369789.1	c.2075+1482G>A		intron_variant		ENST00000591337.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PWWP3A	ENST00000591337.7	c.2075+1482G>A		intron_variant		2	NM_001369789.1	A2

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10952 AN: 152130 Hom.: 541 Cov.: 31

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0719 AC: 10951 AN: 152248 Hom.: 541 Cov.: 31 AF XY: 0.0706 AC XY: 5254 AN XY: 74440

Gnomad4 AFR AF: 0.0189

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0474

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0831 Hom.: 353

Bravo AF: 0.0638

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs6510605; hg19: chr19-1374641;