chr3-142522794-T-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_001184.4(ATR):c.4200A>T(p.Leu1400=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,613,880 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. L1400L) has been classified as Likely benign.
Frequency
Consequence
NM_001184.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATR | NM_001184.4 | c.4200A>T | p.Leu1400= | synonymous_variant | 23/47 | ENST00000350721.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATR | ENST00000350721.9 | c.4200A>T | p.Leu1400= | synonymous_variant | 23/47 | 1 | NM_001184.4 | P1 | |
ATR | ENST00000661310.1 | c.4008A>T | p.Leu1336= | synonymous_variant | 22/46 | ||||
ATR | ENST00000653868.1 | n.4229A>T | non_coding_transcript_exon_variant | 23/35 | |||||
ATR | ENST00000656590.1 | c.2991A>T | p.Leu997= | synonymous_variant, NMD_transcript_variant | 19/44 |
Frequencies
GnomAD3 genomes AF: 0.000888 AC: 135AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251406Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135870
GnomAD4 exome AF: 0.000102 AC: 149AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.0000908 AC XY: 66AN XY: 727152
GnomAD4 genome AF: 0.000900 AC: 137AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.000941 AC XY: 70AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 11, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 08, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
ATR-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Seckel syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at