10-63610317-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001330.3(REEP3):c.548C>T(p.Ala183Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001330.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REEP3 | ENST00000373758.5 | c.548C>T | p.Ala183Val | missense_variant | Exon 6 of 8 | 1 | NM_001001330.3 | ENSP00000362863.4 | ||
REEP3 | ENST00000634963.1 | n.*132C>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 5 | ENSP00000489394.1 | ||||
REEP3 | ENST00000634963.1 | n.*132C>T | 3_prime_UTR_variant | Exon 4 of 6 | 5 | ENSP00000489394.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00 AC: 0AN: 163144 AF XY: 0.00
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1403786Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 692796
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.548C>T (p.A183V) alteration is located in exon 6 (coding exon 6) of the REEP3 gene. This alteration results from a C to T substitution at nucleotide position 548, causing the alanine (A) at amino acid position 183 to be replaced by a valine (V). 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