11-108317539-ATTTT-AT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_000051.4(ATM):c.6347+29_6347+31delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,192,594 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 23)
Exomes 𝑓: 0.000017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ATM
NM_000051.4 intron
NM_000051.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.568
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: Uncertain_significance. The variant received 0 ACMG points.
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.6347+29_6347+31delTTT | intron | N/A | NP_000042.3 | |||
| ATM | NM_001351834.2 | c.6347+29_6347+31delTTT | intron | N/A | NP_001338763.1 | ||||
| C11orf65 | NM_001330368.2 | c.641-8471_641-8469delAAA | 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.6347+19_6347+21delTTT | intron | N/A | ENSP00000501606.1 | |||
| ATM | ENST00000452508.7 | TSL:1 | c.6347+19_6347+21delTTT | intron | N/A | ENSP00000388058.2 | |||
| ATM | ENST00000527805.6 | TSL:1 | n.*1411+19_*1411+21delTTT | intron | N/A | ENSP00000435747.2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 125156Hom.: 0 Cov.: 23
GnomAD3 genomes
AF:
AC:
0
AN:
125156
Hom.:
Cov.:
23
Gnomad AFR
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Gnomad NFE
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GnomAD2 exomes AF: 0.00000981 AC: 1AN: 101888 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
101888
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.0000168 AC: 20AN: 1192594Hom.: 0 AF XY: 0.0000168 AC XY: 10AN XY: 595056 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
20
AN:
1192594
Hom.:
AF XY:
AC XY:
10
AN XY:
595056
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
28912
American (AMR)
AF:
AC:
1
AN:
37656
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21352
East Asian (EAS)
AF:
AC:
1
AN:
30870
South Asian (SAS)
AF:
AC:
3
AN:
73514
European-Finnish (FIN)
AF:
AC:
0
AN:
41402
Middle Eastern (MID)
AF:
AC:
0
AN:
4906
European-Non Finnish (NFE)
AF:
AC:
11
AN:
905082
Other (OTH)
AF:
AC:
1
AN:
48900
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.245
Heterozygous variant carriers
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00 AC: 0AN: 125156Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 59948
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
125156
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
59948
African (AFR)
AF:
AC:
0
AN:
34676
American (AMR)
AF:
AC:
0
AN:
11920
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3070
East Asian (EAS)
AF:
AC:
0
AN:
4258
South Asian (SAS)
AF:
AC:
0
AN:
3950
European-Finnish (FIN)
AF:
AC:
0
AN:
6474
Middle Eastern (MID)
AF:
AC:
0
AN:
256
European-Non Finnish (NFE)
AF:
AC:
0
AN:
58100
Other (OTH)
AF:
AC:
0
AN:
1672
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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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