chr3-142449451-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001184.4(ATR):c.7913T>C(p.Leu2638Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L2638F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATR | NM_001184.4 | c.7913T>C | p.Leu2638Pro | missense_variant | 47/47 | ENST00000350721.9 | |
ATR | NM_001354579.2 | c.7721T>C | p.Leu2574Pro | missense_variant | 46/46 | ||
ATR | XM_011512924.2 | c.7919T>C | p.Leu2640Pro | missense_variant | 47/47 | ||
ATR | XM_011512925.2 | c.7727T>C | p.Leu2576Pro | missense_variant | 46/46 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATR | ENST00000350721.9 | c.7913T>C | p.Leu2638Pro | missense_variant | 47/47 | 1 | NM_001184.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The p.L2638P variant (also known as c.7913T>C), located in coding exon 47 of the ATR gene, results from a T to C substitution at nucleotide position 7913. The leucine at codon 2638 is replaced by proline, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.