chr6-43613848-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006502.3(POLH):c.1433C>T(p.Thr478Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000484 in 1,614,172 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006502.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLH | NM_006502.3 | c.1433C>T | p.Thr478Met | missense_variant | 11/11 | ENST00000372236.9 | NP_006493.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLH | ENST00000372236.9 | c.1433C>T | p.Thr478Met | missense_variant | 11/11 | 1 | NM_006502.3 | ENSP00000361310 | P1 | |
POLH | ENST00000372226.1 | c.*117C>T | 3_prime_UTR_variant | 11/11 | 1 | ENSP00000361300 | ||||
GTPBP2 | ENST00000496137.5 | c.*131+6271G>A | intron_variant, NMD_transcript_variant | 3 | ENSP00000436973 |
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152180Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00152 AC: 383AN: 251428Hom.: 3 AF XY: 0.00152 AC XY: 207AN XY: 135910
GnomAD4 exome AF: 0.000458 AC: 670AN: 1461874Hom.: 3 Cov.: 32 AF XY: 0.000485 AC XY: 353AN XY: 727242
GnomAD4 genome AF: 0.000735 AC: 112AN: 152298Hom.: 1 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74470
ClinVar
Submissions by phenotype
Xeroderma pigmentosum variant type Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 27, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 18, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at