chr10-25024397-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024838.5(THNSL1):c.1174C>T(p.Arg392Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024838.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THNSL1 | NM_024838.5 | c.1174C>T | p.Arg392Cys | missense_variant | 3/3 | ENST00000376356.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THNSL1 | ENST00000376356.5 | c.1174C>T | p.Arg392Cys | missense_variant | 3/3 | 1 | NM_024838.5 | P1 | |
ENKUR | ENST00000615958.4 | c.38-28528G>A | intron_variant | 1 | |||||
THNSL1 | ENST00000524413.5 | c.1174C>T | p.Arg392Cys | missense_variant | 3/3 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251148Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135754
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461556Hom.: 0 Cov.: 40 AF XY: 0.0000289 AC XY: 21AN XY: 727076
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1174C>T (p.R392C) alteration is located in exon 3 (coding exon 1) of the THNSL1 gene. This alteration results from a C to T substitution at nucleotide position 1174, causing the arginine (R) at amino acid position 392 to be replaced by a cysteine (C). 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