11-108317516-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000051.4(ATM):c.6342C>T(p.Ser2114Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000618 in 1,456,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S2114S) has been classified as Benign.
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
ATM
NM_000051.4 synonymous
NM_000051.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.428
Publications
0 publications found
Genes affected
ATM (HGNC:795): (ATM serine/threonine kinase) The protein encoded by this gene belongs to the PI3/PI4-kinase family. This protein is an important cell cycle checkpoint kinase that phosphorylates; thus, it functions as a regulator of a wide variety of downstream proteins, including tumor suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1. This protein and the closely related kinase ATR are thought to be master controllers of cell cycle checkpoint signaling pathways that are required for cell response to DNA damage and for genome stability. Mutations in this gene are associated with ataxia telangiectasia, an autosomal recessive disorder. [provided by RefSeq, Aug 2010]
C11orf65 (HGNC:28519): (chromosome 11 open reading frame 65) Predicted to be involved in negative regulation of mitochondrial fission and negative regulation of protein targeting to mitochondrion. Predicted to be located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 11-108317516-C-T is Benign according to our data. Variant chr11-108317516-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 387701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.428 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000051.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATM | NM_000051.4 | MANE Select | c.6342C>T | p.Ser2114Ser | synonymous | Exon 43 of 63 | NP_000042.3 | ||
| ATM | NM_001351834.2 | c.6342C>T | p.Ser2114Ser | synonymous | Exon 44 of 64 | NP_001338763.1 | |||
| C11orf65 | NM_001330368.2 | c.641-8445G>A | intron | N/A | NP_001317297.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ATM | ENST00000675843.1 | MANE Select | c.6342C>T | p.Ser2114Ser | synonymous | Exon 43 of 63 | ENSP00000501606.1 | ||
| ATM | ENST00000452508.7 | TSL:1 | c.6342C>T | p.Ser2114Ser | synonymous | Exon 44 of 64 | ENSP00000388058.2 | ||
| ATM | ENST00000527805.6 | TSL:1 | n.*1406C>T | non_coding_transcript_exon | Exon 41 of 61 | ENSP00000435747.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
28
GnomAD2 exomes AF: 0.0000120 AC: 3AN: 249160 AF XY: 0.0000223 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
249160
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1456626Hom.: 0 Cov.: 30 AF XY: 0.00000966 AC XY: 7AN XY: 724534 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
1456626
Hom.:
Cov.:
30
AF XY:
AC XY:
7
AN XY:
724534
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33252
American (AMR)
AF:
AC:
1
AN:
44612
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25936
East Asian (EAS)
AF:
AC:
1
AN:
39424
South Asian (SAS)
AF:
AC:
1
AN:
85744
European-Finnish (FIN)
AF:
AC:
0
AN:
52910
Middle Eastern (MID)
AF:
AC:
0
AN:
5734
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1108982
Other (OTH)
AF:
AC:
1
AN:
60032
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.469
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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50-55
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
28
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Benign/Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
2
Hereditary cancer-predisposing syndrome (2)
-
-
2
not specified (2)
-
-
1
Ataxia-telangiectasia syndrome (1)
-
-
1
ATM-related disorder (1)
-
-
1
Familial cancer of breast (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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