chr17-75640856-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001162995.3(SMIM5):c.193C>T(p.Arg65Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,548,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001162995.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMIM5 | NM_001162995.3 | c.193C>T | p.Arg65Trp | missense_variant | Exon 3 of 3 | ENST00000375215.3 | NP_001156467.1 | |
RECQL5 | NM_004259.7 | c.1230-9188G>A | intron_variant | Intron 8 of 19 | ENST00000317905.10 | NP_004250.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMIM5 | ENST00000375215.3 | c.193C>T | p.Arg65Trp | missense_variant | Exon 3 of 3 | 1 | NM_001162995.3 | ENSP00000364363.3 | ||
RECQL5 | ENST00000317905.10 | c.1230-9188G>A | intron_variant | Intron 8 of 19 | 1 | NM_004259.7 | ENSP00000317636.5 | |||
RECQL5 | ENST00000423245.6 | c.1149-9188G>A | intron_variant | Intron 8 of 19 | 1 | ENSP00000394820.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000454 AC: 7AN: 154016Hom.: 0 AF XY: 0.0000733 AC XY: 6AN XY: 81834
GnomAD4 exome AF: 0.0000294 AC: 41AN: 1396314Hom.: 0 Cov.: 31 AF XY: 0.0000407 AC XY: 28AN XY: 688750
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.193C>T (p.R65W) alteration is located in exon 3 (coding exon 2) of the SMIM5 gene. This alteration results from a C to T substitution at nucleotide position 193, causing the arginine (R) at amino acid position 65 to be replaced by a tryptophan (W). 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