20-32014949-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365692.1(CCM2L):c.76C>T(p.Arg26Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000556 in 1,601,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365692.1 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 |
---|---|---|---|---|---|---|---|---|
CCM2L | NM_001365692.1 | c.76C>T | p.Arg26Cys | missense_variant | Exon 2 of 10 | ENST00000452892.3 | NP_001352621.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCM2L | ENST00000452892.3 | c.76C>T | p.Arg26Cys | missense_variant | Exon 2 of 10 | 2 | NM_001365692.1 | ENSP00000392448.2 | ||
CCM2L | ENST00000262659.12 | c.76C>T | p.Arg26Cys | missense_variant | Exon 2 of 9 | 1 | ENSP00000262659.8 | |||
ENSG00000226239 | ENST00000653258.1 | n.705-7300G>A | intron_variant | Intron 2 of 2 | ||||||
ENSG00000226239 | ENST00000662576.1 | n.816-7300G>A | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000887 AC: 21AN: 236886Hom.: 0 AF XY: 0.000124 AC XY: 16AN XY: 128836
GnomAD4 exome AF: 0.0000566 AC: 82AN: 1449760Hom.: 0 Cov.: 31 AF XY: 0.0000818 AC XY: 59AN XY: 721314
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.76C>T (p.R26C) alteration is located in exon 2 (coding exon 2) of the CCM2L gene. This alteration results from a C to T substitution at nucleotide position 76, causing the arginine (R) at amino acid position 26 to be replaced by a cysteine (C). 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