NM_052862.4:c.124C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052862.4(RCSD1):c.124C>T(p.Pro42Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RCSD1 | NM_052862.4 | c.124C>T | p.Pro42Ser | missense_variant | Exon 3 of 7 | ENST00000367854.8 | NP_443094.3 | |
RCSD1 | NM_001322923.2 | c.108+1435C>T | intron_variant | Intron 2 of 5 | NP_001309852.1 | |||
RCSD1 | NM_001322924.2 | c.108+1435C>T | intron_variant | Intron 2 of 4 | NP_001309853.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RCSD1 | ENST00000367854.8 | c.124C>T | p.Pro42Ser | missense_variant | Exon 3 of 7 | 1 | NM_052862.4 | ENSP00000356828.3 | ||
RCSD1 | ENST00000537350.5 | c.108+1435C>T | intron_variant | Intron 2 of 5 | 1 | ENSP00000439409.1 | ||||
RCSD1 | ENST00000361496.3 | c.124C>T | p.Pro42Ser | missense_variant | Exon 3 of 5 | 3 | ENSP00000355291.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461564Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727082
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124C>T (p.P42S) alteration is located in exon 3 (coding exon 3) of the RCSD1 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the proline (P) at amino acid position 42 to be replaced by a serine (S). 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