16-2039932-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002528.7(NTHL1):c.907G>A(p.Gly303Ser) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G303R) has been classified as Likely benign.
Frequency
Consequence
NM_002528.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTHL1 | NM_002528.7 | c.907G>A | p.Gly303Ser | missense_variant | 6/6 | ENST00000651570.2 | |
NTHL1 | NM_001318193.2 | c.736G>A | p.Gly246Ser | missense_variant | 5/5 | ||
NTHL1 | NM_001318194.2 | c.577G>A | p.Gly193Ser | missense_variant | 6/6 | ||
NTHL1 | XM_047434171.1 | c.628G>A | p.Gly210Ser | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTHL1 | ENST00000651570.2 | c.907G>A | p.Gly303Ser | missense_variant | 6/6 | NM_002528.7 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1450248Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 721750
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2022 | The p.G311S variant (also known as c.931G>A), located in coding exon 6 of the NTHL1 gene, results from a G to A substitution at nucleotide position 931. The glycine at codon 311 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.