chr18-32204306-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_005925.3(MEP1B):c.493T>A(p.Ser165Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,451,816 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. S165L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005925.3 missense
Scores
Clinical Significance
Conservation
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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.493T>A | p.Ser165Thr | missense_variant | 7/15 | ENST00000269202.11 | |
MEP1B | NM_001308171.2 | c.493T>A | p.Ser165Thr | missense_variant | 7/15 | ||
MEP1B | XM_011526013.3 | c.493T>A | p.Ser165Thr | missense_variant | 7/14 | ||
MEP1B | XM_011526014.3 | c.493T>A | p.Ser165Thr | missense_variant | 7/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1B | ENST00000269202.11 | c.493T>A | p.Ser165Thr | missense_variant | 7/15 | 1 | NM_005925.3 | P4 | |
MEP1B | ENST00000581447.1 | c.493T>A | p.Ser165Thr | missense_variant | 7/15 | 1 | A1 | ||
GAREM1 | ENST00000583696.1 | c.66-67846A>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1451816Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 720960
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.493T>A (p.S165T) alteration is located in exon 7 (coding exon 7) of the MEP1B gene. This alteration results from a T to A substitution at nucleotide position 493, causing the serine (S) at amino acid position 165 to be replaced by a threonine (T). 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