chr1-167694237-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052862.4(RCSD1):c.409G>A(p.Ala137Thr) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052862.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RCSD1 | NM_052862.4 | c.409G>A | p.Ala137Thr | missense_variant | Exon 5 of 7 | ENST00000367854.8 | NP_443094.3 | |
RCSD1 | NM_001322923.2 | c.319G>A | p.Ala107Thr | missense_variant | Exon 4 of 6 | NP_001309852.1 | ||
RCSD1 | NM_001322924.2 | c.247G>A | p.Ala83Thr | missense_variant | Exon 3 of 5 | NP_001309853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RCSD1 | ENST00000367854.8 | c.409G>A | p.Ala137Thr | missense_variant | Exon 5 of 7 | 1 | NM_052862.4 | ENSP00000356828.3 | ||
RCSD1 | ENST00000537350.5 | c.319G>A | p.Ala107Thr | missense_variant | Exon 4 of 6 | 1 | ENSP00000439409.1 | |||
RCSD1 | ENST00000361496.3 | c.337G>A | p.Ala113Thr | missense_variant | Exon 4 of 5 | 3 | ENSP00000355291.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.409G>A (p.A137T) alteration is located in exon 5 (coding exon 5) of the RCSD1 gene. This alteration results from a G to A substitution at nucleotide position 409, causing the alanine (A) at amino acid position 137 to be replaced by a threonine (T). 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