chr6-108899778-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032131.6(ARMC2):c.833G>A(p.Arg278His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,611,858 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032131.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC2 | NM_032131.6 | c.833G>A | p.Arg278His | missense_variant | 7/18 | ENST00000392644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC2 | ENST00000392644.9 | c.833G>A | p.Arg278His | missense_variant | 7/18 | 1 | NM_032131.6 | P1 | |
ARMC2 | ENST00000368972.7 | c.338G>A | p.Arg113His | missense_variant | 6/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 151816Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249138Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134630
GnomAD4 exome AF: 0.000147 AC: 215AN: 1460042Hom.: 1 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 726260
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 151816Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74130
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at