4-90308324-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001145065.2(CCSER1):c.40C>T(p.Arg14Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000499 in 1,602,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145065.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCSER1 | ENST00000509176.6 | c.40C>T | p.Arg14Trp | missense_variant | Exon 2 of 11 | 1 | NM_001145065.2 | ENSP00000425040.1 | ||
CCSER1 | ENST00000432775.6 | c.40C>T | p.Arg14Trp | missense_variant | Exon 2 of 8 | 1 | ENSP00000389283.2 | |||
CCSER1 | ENST00000505073.5 | n.40C>T | non_coding_transcript_exon_variant | Exon 2 of 10 | 1 | ENSP00000420964.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 230478Hom.: 0 AF XY: 0.0000161 AC XY: 2AN XY: 124428
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450324Hom.: 0 Cov.: 32 AF XY: 0.00000694 AC XY: 5AN XY: 720226
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.40C>T (p.R14W) alteration is located in exon 2 (coding exon 1) of the CCSER1 gene. This alteration results from a C to T substitution at nucleotide position 40, causing the arginine (R) at amino acid position 14 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