chr6-108876230-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032131.6(ARMC2):c.551C>T(p.Ala184Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000283 in 1,612,734 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_032131.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC2 | NM_032131.6 | c.551C>T | p.Ala184Val | missense_variant | 5/18 | ENST00000392644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC2 | ENST00000392644.9 | c.551C>T | p.Ala184Val | missense_variant | 5/18 | 1 | NM_032131.6 | P1 | |
ARMC2 | ENST00000368972.7 | c.56C>T | p.Ala19Val | missense_variant | 4/17 | 2 | |||
ARMC2 | ENST00000237512.4 | c.551C>T | p.Ala184Val | missense_variant | 5/5 | 2 | |||
ARMC2 | ENST00000414610.1 | c.107C>T | p.Ala36Val | missense_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000539 AC: 82AN: 152152Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000972 AC: 243AN: 249928Hom.: 1 AF XY: 0.000933 AC XY: 126AN XY: 135034
GnomAD4 exome AF: 0.000255 AC: 373AN: 1460464Hom.: 3 Cov.: 31 AF XY: 0.000242 AC XY: 176AN XY: 726404
GnomAD4 genome ? AF: 0.000545 AC: 83AN: 152270Hom.: 1 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74454
ClinVar
Submissions by phenotype
ARMC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 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