chr1-167697280-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052862.4(RCSD1):c.656C>T(p.Ser219Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,094 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_052862.4 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 |
---|---|---|---|---|---|---|---|
RCSD1 | NM_052862.4 | c.656C>T | p.Ser219Phe | missense_variant | 6/7 | ENST00000367854.8 | |
RCSD1 | NM_001322923.2 | c.566C>T | p.Ser189Phe | missense_variant | 5/6 | ||
RCSD1 | NM_001322924.2 | c.494C>T | p.Ser165Phe | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCSD1 | ENST00000367854.8 | c.656C>T | p.Ser219Phe | missense_variant | 6/7 | 1 | NM_052862.4 | P2 | |
RCSD1 | ENST00000537350.5 | c.566C>T | p.Ser189Phe | missense_variant | 5/6 | 1 | A2 | ||
RCSD1 | ENST00000361496.3 | c.584C>T | p.Ser195Phe | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.656C>T (p.S219F) alteration is located in exon 6 (coding exon 6) of the RCSD1 gene. This alteration results from a C to T substitution at nucleotide position 656, causing the serine (S) at amino acid position 219 to be replaced by a phenylalanine (F). 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