18-32204307-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_005925.3(MEP1B):c.494C>T(p.Ser165Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,603,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. S165T) has been classified as Uncertain significance.
Frequency
Consequence
NM_005925.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEP1B | NM_005925.3 | c.494C>T | p.Ser165Leu | missense_variant | 7/15 | ENST00000269202.11 | |
MEP1B | NM_001308171.2 | c.494C>T | p.Ser165Leu | missense_variant | 7/15 | ||
MEP1B | XM_011526013.3 | c.494C>T | p.Ser165Leu | missense_variant | 7/14 | ||
MEP1B | XM_011526014.3 | c.494C>T | p.Ser165Leu | missense_variant | 7/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1B | ENST00000269202.11 | c.494C>T | p.Ser165Leu | missense_variant | 7/15 | 1 | NM_005925.3 | P4 | |
MEP1B | ENST00000581447.1 | c.494C>T | p.Ser165Leu | missense_variant | 7/15 | 1 | A1 | ||
GAREM1 | ENST00000583696.1 | c.66-67847G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151922Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000861 AC: 2AN: 232326Hom.: 0 AF XY: 0.00000798 AC XY: 1AN XY: 125352
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1451396Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 13AN XY: 720696
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151922Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74202
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 09, 2022 | The c.494C>T (p.S165L) alteration is located in exon 7 (coding exon 7) of the MEP1B gene. This alteration results from a C to T substitution at nucleotide position 494, causing the serine (S) at amino acid position 165 to be replaced by a leucine (L). 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