rs2953983

Positions:

• chr8-42355738-G-A
• chr8-42355738-G-C

Variant summary

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

The NM_002690.3(POLB):​c.422+171G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,204 control chromosomes in the GnomAD database, including 48,300 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 0.76 (48300 hom., cov: 33)
• Consequence: POLB NM_002690.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

POLB (HGNC:9174): (DNA polymerase beta) The protein encoded by this gene is a DNA polymerase involved in base excision and repair, also called gap-filling DNA synthesis. The encoded protein, acting as a monomer, is normally found in the cytoplasm, but it translocates to the nucleus upon DNA damage. Several transcript variants of this gene exist, but the full-length nature of only one has been described to date. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLB	NM_002690.3	c.422+171G>A		intron_variant		ENST00000265421.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLB	ENST00000265421.9	c.422+171G>A		intron_variant		1	NM_002690.3	P1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115966 AN: 152086 Hom.: 48283 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.762 AC: 116011 AN: 152204 Hom.: 48300 Cov.: 33 AF XY: 0.760 AC XY: 56580 AN XY: 74416

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.803

Alfa AF: 0.830 Hom.: 6888

Bravo AF: 0.755

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.52

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: rs2953983; hg19: chr8-42213256;