15-52584818-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001385016.1(ATOSA):​c.3004G>A​(p.Val1002Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

ATOSA
NM_001385016.1 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.126
Variant links:
Genes affected
ATOSA (HGNC:25609): (atos homolog A)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.016536474).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATOSANM_001385016.1 linkc.3004G>A p.Val1002Met missense_variant Exon 12 of 13 ENST00000619572.5 NP_001371945.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATOSAENST00000619572.5 linkc.3004G>A p.Val1002Met missense_variant Exon 12 of 13 1 NM_001385016.1 ENSP00000484641.1 Q32MH5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000282
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.056
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
10
DANN
Benign
0.88
DEOGEN2
Benign
0.00024
T;.;T;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.22
N
LIST_S2
Benign
0.36
.;T;T;T
M_CAP
Benign
0.0026
T
MetaRNN
Benign
0.017
T;T;T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
-1.2
N;.;N;.
PrimateAI
Benign
0.33
T
PROVEAN
Benign
0.030
N;N;.;N
REVEL
Benign
0.014
Sift
Benign
1.0
T;T;.;T
Sift4G
Benign
0.57
T;T;T;.
Polyphen
0.0
B;.;B;.
Vest4
0.13
MutPred
0.22
Loss of methylation at K1003 (P = 0.0321);.;Loss of methylation at K1003 (P = 0.0321);.;
MVP
0.14
MPC
0.089
ClinPred
0.16
T
GERP RS
1.2
Varity_R
0.019
gMVP
0.086

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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: rs942413773; hg19: chr15-52877015; COSMIC: COSV55922296; COSMIC: COSV55922296; API