6-149889576-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394057.1(RAET1E):c.394C>T(p.Arg132Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,614,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. 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. R132Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001394057.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAET1E | NM_001394057.1 | c.394C>T | p.Arg132Trp | missense_variant | 5/6 | ENST00000357183.9 | |
RAET1E-LRP11 | NR_182438.1 | n.812C>T | non_coding_transcript_exon_variant | 4/15 | |||
RAET1E-AS1 | NR_045126.1 | n.885+25194G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAET1E | ENST00000357183.9 | c.394C>T | p.Arg132Trp | missense_variant | 5/6 | 1 | NM_001394057.1 | P2 | |
RAET1E-AS1 | ENST00000605899.1 | n.114+3903G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
RAET1E-AS1 | ENST00000606915.1 | n.889+25194G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251328Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135824
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461882Hom.: 0 Cov.: 40 AF XY: 0.0000330 AC XY: 24AN XY: 727242
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.394C>T (p.R132W) alteration is located in exon 1 (coding exon 1) of the RAET1E gene. This alteration results from a C to T substitution at nucleotide position 394, causing the arginine (R) at amino acid position 132 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at