chr20-57367077-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003610.4(RAE1):c.532G>A(p.Val178Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000019 in 1,576,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003610.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000456 AC: 11AN: 241292Hom.: 0 AF XY: 0.0000691 AC XY: 9AN XY: 130316
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1424262Hom.: 0 Cov.: 31 AF XY: 0.0000183 AC XY: 13AN XY: 709928
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.532G>A (p.V178M) alteration is located in exon 7 (coding exon 6) of the RAE1 gene. This alteration results from a G to A substitution at nucleotide position 532, causing the valine (V) at amino acid position 178 to be replaced by a methionine (M). 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