6-43605330-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006502.3(POLH):c.1074+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
POLH
NM_006502.3 intron
NM_006502.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.425
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 6-43605330-C-T is Benign according to our data. Variant chr6-43605330-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3645467.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLH | NM_006502.3 | c.1074+11C>T | intron_variant | Intron 9 of 10 | ENST00000372236.9 | NP_006493.1 | ||
POLH | NM_001291969.2 | c.702+11C>T | intron_variant | Intron 7 of 8 | NP_001278898.1 | |||
POLH | NM_001291970.2 | c.1074+11C>T | intron_variant | Intron 9 of 10 | NP_001278899.1 | |||
POLH | XM_047418900.1 | c.618+11C>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+11C>T | intron_variant | Intron 9 of 10 | 1 | NM_006502.3 | ENSP00000361310.4 | |||
POLH | ENST00000372226.1 | c.1074+11C>T | intron_variant | Intron 9 of 10 | 1 | ENSP00000361300.1 | ||||
GTPBP2 | ENST00000496137.5 | n.*184G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 | ENSP00000436973.1 | ||||
GTPBP2 | ENST00000496137.5 | n.*184G>A | 3_prime_UTR_variant | Exon 4 of 4 | 3 | ENSP00000436973.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1362438Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 683086
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1362438
Hom.:
Cov.:
21
AF XY:
AC XY:
0
AN XY:
683086
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 12, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at