6-43605580-C-T

Variant names:

• chr6-43605580-C-T
• rs140119541
• NM_006502.3:c.1074+261C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_006502.3(POLH):​c.1074+261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 151,232 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.013 (16 hom., cov: 30)
• Consequence: POLH NM_006502.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.681

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]

GTPBP2 (HGNC:4670): (GTP binding protein 2) GTP-binding proteins, or G proteins, constitute a superfamily capable of binding GTP or GDP. G proteins are activated by binding GTP and are inactivated by hydrolyzing GTP to GDP. This general mechanism enables G proteins to perform a wide range of biologic activities.[supplied by OMIM, Jan 2003]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 6-43605580-C-T is Benign according to our data. Variant chr6-43605580-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1207530.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0126 (1904/151232) while in subpopulation NFE AF = 0.0207 (1404/67818). AF 95% confidence interval is 0.0198. There are 16 homozygotes in GnomAd4. There are 852 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLH	NM_006502.3	c.1074+261C>T		intron_variant	Intron 9 of 10	ENST00000372236.9	NP_006493.1
POLH	NM_001291969.2	c.702+261C>T		intron_variant	Intron 7 of 8		NP_001278898.1
POLH	NM_001291970.2	c.1074+261C>T		intron_variant	Intron 9 of 10		NP_001278899.1
POLH	XM_047418900.1	c.618+261C>T		intron_variant	Intron 6 of 7		XP_047274856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLH	ENST00000372236.9	c.1074+261C>T		intron_variant	Intron 9 of 10	1	NM_006502.3	ENSP00000361310.4
POLH	ENST00000372226.1	c.1074+261C>T		intron_variant	Intron 9 of 10	1		ENSP00000361300.1
GTPBP2	ENST00000496137.5	n.*132-198G>A		intron_variant	Intron 3 of 3	3		ENSP00000436973.1

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1904 AN: 151110 Hom.: 16 Cov.: 30

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.000975

Gnomad SAS AF: 0.000418

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0116

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

GnomAD4 genome AF: 0.0126 AC: 1904 AN: 151232 Hom.: 16 Cov.: 30 AF XY: 0.0115 AC XY: 852 AN XY: 73798

Gnomad4 AFR AF: 0.00330 AC: 0.00329729 AN: 0.00329729

Gnomad4 AMR AF: 0.0107 AC: 0.0106973 AN: 0.0106973

Gnomad4 ASJ AF: 0.0219 AC: 0.02194 AN: 0.02194

Gnomad4 EAS AF: 0.000978 AC: 0.000977708 AN: 0.000977708

Gnomad4 SAS AF: 0.000418 AC: 0.000417885 AN: 0.000417885

Gnomad4 FIN AF: 0.00820 AC: 0.00820305 AN: 0.00820305

Gnomad4 NFE AF: 0.0207 AC: 0.0207025 AN: 0.0207025

Gnomad4 OTH AF: 0.0114 AC: 0.0114395 AN: 0.0114395

Alfa AF: 0.0132 Hom.: 1

Bravo AF: 0.0128

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.18
Mutation Taster		=100/0	polymorphism

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: rs140119541; hg19: chr6-43573317;