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rs4986761

chr11-108254034-T-Achr11-108254034-T-C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2_SupportingPM5BP4_Strong

The NM_000051(ATM):c.2119T>A(p.Ser707Thr) 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. 14/20 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. S707P) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

ATM
NM_000051 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.160

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 32.
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr11-108254034-T-C is described in Lovd as [Pathogenic].
BP4
?
Computational evidence support a benign effect (MetaRNN=0.06426412).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATMNM_000051.4 linkuse as main transcriptc.2119T>A p.Ser707Thr missense_variant 13/63 ENST00000675843.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATMENST00000675843.1 linkuse as main transcriptc.2119T>A p.Ser707Thr missense_variant 13/63 NM_000051.4 P1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.087
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
Cadd
Benign
5.1
Dann
Benign
0.66
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.49
FATHMM_MKL
Benign
0.27
N
LIST_S2
Benign
0.67
T;T;.
M_CAP
Benign
0.034
D
MetaRNN
Benign
0.064
T;T;T
MetaSVM
Benign
-0.88
T
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-0.61
N;N;N
REVEL
Benign
0.27
Sift
Benign
0.76
T;T;T
Sift4G
Benign
0.31
T;T;T
Polyphen
0.0040
.;B;B
Vest4
0.27, 0.26
MutPred
0.16
Loss of disorder (P = 0.0674);Loss of disorder (P = 0.0674);Loss of disorder (P = 0.0674);
MVP
0.75
MPC
0.16
ClinPred
0.18
T
GERP RS
3.8
Varity_R
0.11
gMVP
0.080

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-108124761;