chr6-108876176-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032131.6(ARMC2):c.497T>C(p.Met166Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,611,400 control chromosomes in the GnomAD database, including 2,500 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032131.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC2 | NM_032131.6 | c.497T>C | p.Met166Thr | missense_variant | 5/18 | ENST00000392644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC2 | ENST00000392644.9 | c.497T>C | p.Met166Thr | missense_variant | 5/18 | 1 | NM_032131.6 | P1 | |
ARMC2 | ENST00000368972.7 | c.2T>C | p.Met1? | start_lost | 4/17 | 2 | |||
ARMC2 | ENST00000237512.4 | c.497T>C | p.Met166Thr | missense_variant | 5/5 | 2 | |||
ARMC2 | ENST00000414610.1 | c.53T>C | p.Met18Thr | missense_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0322 AC: 4893AN: 152164Hom.: 220 Cov.: 32
GnomAD3 exomes AF: 0.0566 AC: 14077AN: 248588Hom.: 893 AF XY: 0.0586 AC XY: 7868AN XY: 134330
GnomAD4 exome AF: 0.0337 AC: 49234AN: 1459118Hom.: 2279 Cov.: 31 AF XY: 0.0364 AC XY: 26436AN XY: 725680
GnomAD4 genome ? AF: 0.0322 AC: 4905AN: 152282Hom.: 221 Cov.: 32 AF XY: 0.0372 AC XY: 2773AN XY: 74452
ClinVar
Submissions by phenotype
ARMC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at