chr15-52584818-C-T

Variant names:

• chr15-52584818-C-T
• rs942413773
• NM_001385016.1:c.3004G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1002L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATOSA NM_001385016.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

ATOSA (HGNC:25609): (atos homolog A)

ENSG00000260618 (HGNC:):

ACMG classification

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
ATOSA	NM_001385016.1	c.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
ATOSA	ENST00000619572.5	c.3004G>A	p.Val1002Met	missense_variant	Exon 12 of 13	1	NM_001385016.1	ENSP00000484641.1

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

Other links and lift over

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