chr6-44169433-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_007058.4(CAPN11):c.241G>A(p.Glu81Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007058.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN11 | ENST00000398776.2 | c.241G>A | p.Glu81Lys | missense_variant | Exon 3 of 23 | 1 | NM_007058.4 | ENSP00000381758.1 | ||
CAPN11 | ENST00000532171.5 | c.331G>A | p.Glu111Lys | missense_variant | Exon 4 of 6 | 4 | ENSP00000432420.1 | |||
CAPN11 | ENST00000526118.1 | n.*253G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 4 | ENSP00000431963.1 | ||||
CAPN11 | ENST00000526118.1 | n.*253G>A | 3_prime_UTR_variant | Exon 4 of 5 | 4 | ENSP00000431963.1 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152144Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000486 AC: 12AN: 246948 AF XY: 0.0000596 show subpopulations
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1460968Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 726708 show subpopulations
GnomAD4 genome AF: 0.000322 AC: 49AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74450 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.241G>A (p.E81K) alteration is located in exon 3 (coding exon 3) of the CAPN11 gene. This alteration results from a G to A substitution at nucleotide position 241, causing the glutamic acid (E) at amino acid position 81 to be replaced by a lysine (K). 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