chr1-236762602-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PP3_ModerateBP6BS2
The NM_001103.4(ACTN2):c.2668G>A(p.Gly890Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,062 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001103.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACTN2 | NM_001103.4 | c.2668G>A | p.Gly890Arg | missense_variant | Exon 21 of 21 | ENST00000366578.6 | NP_001094.1 | |
ACTN2 | NM_001278343.2 | c.2668G>A | p.Gly890Arg | missense_variant | Exon 21 of 21 | NP_001265272.1 | ||
ACTN2 | NR_184402.1 | n.3040G>A | non_coding_transcript_exon_variant | Exon 23 of 23 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251106Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135736
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461792Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727202
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74438
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The p.G890R variant (also known as c.2668G>A), located in coding exon 21 of the ACTN2 gene, results from a G to A substitution at nucleotide position 2668. The glycine at codon 890 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Primary familial hypertrophic cardiomyopathy;C2677338:Dilated cardiomyopathy 1AA Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at