chr10-122454932-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001099667.3(ARMS2):c.205G>T(p.Ala69Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,613,268 control chromosomes in the GnomAD database, including 44,676 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001099667.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMS2 | NM_001099667.3 | c.205G>T | p.Ala69Ser | missense_variant | 1/2 | ENST00000528446.1 | |
LOC105378525 | XR_946382.3 | n.1874+3563C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMS2 | ENST00000528446.1 | c.205G>T | p.Ala69Ser | missense_variant | 1/2 | 1 | NM_001099667.3 | P1 | |
ENST00000650300.1 | n.1852+3563C>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000647969.1 | n.182+3563C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35599AN: 151862Hom.: 4374 Cov.: 31
GnomAD3 exomes AF: 0.255 AC: 63112AN: 247210Hom.: 8554 AF XY: 0.255 AC XY: 34187AN XY: 134312
GnomAD4 exome AF: 0.230 AC: 336596AN: 1461288Hom.: 40295 Cov.: 36 AF XY: 0.232 AC XY: 168758AN XY: 726930
GnomAD4 genome ? AF: 0.234 AC: 35639AN: 151980Hom.: 4381 Cov.: 31 AF XY: 0.237 AC XY: 17612AN XY: 74280
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1Other:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 17, 2019 | This variant is associated with the following publications: (PMID: 17903296, 30389424, 28173125, 16642439, 23274582, 24036949, 20664795, 21203342, 21031019, 22232482, 21825189, 19823576, 19898184, 21397333, 16174643, 20688737, 16936732, 20378180, 20042647, 20381870, 17884985, 20574013, 19933195, 19268887, 21236409, 22893087, 18164066, 23326481, 22509112, 23112567, 21106043) - |
not provided, no classification provided | not provided | Department of Ophthalmology and Visual Sciences Kyoto University | - | - - |
Age related macular degeneration 8 Benign:1Other:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2013 | - - |
ARMS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 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