6-149889516-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394057.1(RAET1E):c.454G>T(p.Ala152Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,014 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 (★).
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.454G>T | p.Ala152Ser | missense_variant | 5/6 | ENST00000357183.9 | |
RAET1E-LRP11 | NR_182438.1 | n.872G>T | non_coding_transcript_exon_variant | 4/15 | |||
RAET1E-AS1 | NR_045126.1 | n.885+25134C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAET1E | ENST00000357183.9 | c.454G>T | p.Ala152Ser | missense_variant | 5/6 | 1 | NM_001394057.1 | P2 | |
RAET1E-AS1 | ENST00000605899.1 | n.114+3843C>A | intron_variant, non_coding_transcript_variant | 5 | |||||
RAET1E-AS1 | ENST00000606915.1 | n.889+25134C>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251418Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135878
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461890Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.454G>T (p.A152S) alteration is located in exon 1 (coding exon 1) of the RAET1E gene. This alteration results from a G to T substitution at nucleotide position 454, causing the alanine (A) at amino acid position 152 to be replaced by a serine (S). 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