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GeneBe

rs10490924

chr10-122454932-G-Cchr10-122454932-G-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_001099667(ARMS2):c.205G>C(p.Ala69Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A69S) has been classified as Benign.

Frequency

Genomes: not found (cov: 31)

Consequence

ARMS2
NM_001099667 missense

Scores

3
1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.119980395).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARMS2NM_001099667.3 linkuse as main transcriptc.205G>C p.Ala69Pro missense_variant 1/2 ENST00000528446.1
LOC105378525XR_946382.3 linkuse as main transcriptn.1874+3563C>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARMS2ENST00000528446.1 linkuse as main transcriptc.205G>C p.Ala69Pro missense_variant 1/21 NM_001099667.3 P1
ENST00000650300.1 linkuse as main transcriptn.1852+3563C>G intron_variant, non_coding_transcript_variant
ENST00000647969.1 linkuse as main transcriptn.182+3563C>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.42
Cadd
Benign
18
Dann
Benign
0.97
DEOGEN2
Benign
0.035
T
Eigen
Benign
-0.80
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.0058
N
LIST_S2
Benign
0.43
T
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.0
N
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.31
T
PROVEAN
Pathogenic
-4.6
D
REVEL
Benign
0.094
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.45
B
Vest4
0.32
MutPred
0.40
Loss of helix (P = 0.0041);
MVP
0.048
MPC
1.5
ClinPred
0.49
T
GERP RS
1.0
Varity_R
0.61
gMVP
0.032

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10490924; hg19: chr10-124214448;