rs767433001

Variant names:

• chr6-43587489-G-A
• rs767433001
• NM_006502.3:c.490G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43587489-G-A
• chr6-43587489-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PP3_Strong

The NM_006502.3(POLH):​c.490G>A​(p.Glu164Lys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: POLH NM_006502.3 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.14

Genes affected

POLH (HGNC:9181): (DNA polymerase eta) This gene encodes a member of the Y family of specialized DNA polymerases. It copies undamaged DNA with a lower fidelity than other DNA-directed polymerases. However, it accurately replicates UV-damaged DNA; when thymine dimers are present, this polymerase inserts the complementary nucleotides in the newly synthesized DNA, thereby bypassing the lesion and suppressing the mutagenic effect of UV-induced DNA damage. This polymerase is thought to be involved in hypermutation during immunoglobulin class switch recombination. Mutations in this gene result in XPV, a variant type of xeroderma pigmentosum. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a domain UmuC (size 250) in uniprot entity POLH_HUMAN there are 6 pathogenic changes around while only 1 benign (86%) in NM_006502.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLH	NM_006502.3	c.490G>A	p.Glu164Lys	missense_variant, splice_region_variant	Exon 4 of 11	ENST00000372236.9	NP_006493.1
POLH	NM_001291970.2	c.490G>A	p.Glu164Lys	missense_variant, splice_region_variant	Exon 4 of 11		NP_001278899.1
POLH	XM_047418900.1	c.-130G>A		5_prime_UTR_variant	Exon 1 of 8		XP_047274856.1
POLH	NM_001291969.2	c.118+4348G>A		intron_variant	Intron 2 of 8		NP_001278898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLH	ENST00000372236.9	c.490G>A	p.Glu164Lys	missense_variant, splice_region_variant	Exon 4 of 11	1	NM_006502.3	ENSP00000361310.4
POLH	ENST00000372226.1	c.490G>A	p.Glu164Lys	missense_variant, splice_region_variant	Exon 4 of 11	1		ENSP00000361300.1
POLH	ENST00000443535.1	c.*89G>A		downstream_gene_variant		2		ENSP00000405320.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Pathogenic	31
DANN	Uncertain	1.0
DEOGEN2	Benign	0.26	T;.
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Benign	0.74	T;T
M_CAP	Benign	0.022	T
MetaRNN	Benign	0.37	T;T
MetaSVM	Benign	-0.84	T
MutationAssessor	Benign	2.0	M;M
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.9	N;N
REVEL	Benign	0.29
Sift	Benign	0.048	D;T
Sift4G	Uncertain	0.031	D;T
Polyphen		0.080	B;.
Vest4		0.50
MutPred		0.51		Gain of methylation at E164 (P = 0.0112);Gain of methylation at E164 (P = 0.0112);
MVP		0.78
MPC		0.25
ClinPred		0.83	D
GERP RS		5.6
Varity_R		0.44
gMVP		0.67

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.90		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.90		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs767433001; hg19: chr6-43555226;