3-142347276-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282857.2(XRN1):āc.3835A>Gā(p.Ser1279Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,608,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001282857.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRN1 | NM_001282857.2 | c.3835A>G | p.Ser1279Gly | missense_variant | 33/41 | ENST00000392981.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRN1 | ENST00000392981.7 | c.3835A>G | p.Ser1279Gly | missense_variant | 33/41 | 1 | NM_001282857.2 | P3 | |
XRN1 | ENST00000264951.8 | c.3835A>G | p.Ser1279Gly | missense_variant | 33/42 | 1 | A2 | ||
XRN1 | ENST00000498077.6 | c.2233A>G | p.Ser745Gly | missense_variant | 19/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249194Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134714
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456706Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 2AN XY: 724462
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.3835A>G (p.S1279G) alteration is located in exon 33 (coding exon 33) of the XRN1 gene. This alteration results from a A to G substitution at nucleotide position 3835, causing the serine (S) at amino acid position 1279 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at