10-122454920-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099667.3(ARMS2):āc.193A>Gā(p.Met65Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001099667.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMS2 | NM_001099667.3 | c.193A>G | p.Met65Val | missense_variant | 1/2 | ENST00000528446.1 | NP_001093137.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMS2 | ENST00000528446.1 | c.193A>G | p.Met65Val | missense_variant | 1/2 | 1 | NM_001099667.3 | ENSP00000436682.1 | ||
ENSG00000285955 | ENST00000647969.1 | n.182+3575T>C | intron_variant | |||||||
ENSG00000285955 | ENST00000650300.1 | n.1852+3575T>C | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247740Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134560
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461680Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727128
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.193A>G (p.M65V) alteration is located in exon 1 (coding exon 1) of the ARMS2 gene. This alteration results from a A to G substitution at nucleotide position 193, causing the methionine (M) at amino acid position 65 to be replaced by a valine (V). 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