15-89750706-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018670.4(MESP1):c.526A>T(p.Thr176Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,381,292 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_018670.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MESP1 | NM_018670.4 | c.526A>T | p.Thr176Ser | missense_variant | 1/2 | ENST00000300057.5 | NP_061140.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MESP1 | ENST00000300057.5 | c.526A>T | p.Thr176Ser | missense_variant | 1/2 | 1 | NM_018670.4 | ENSP00000300057.4 | ||
MESP1 | ENST00000559894.1 | n.114+318A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152108Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000521 AC: 20AN: 38352Hom.: 0 AF XY: 0.000316 AC XY: 7AN XY: 22148
GnomAD4 exome AF: 0.000195 AC: 240AN: 1229076Hom.: 2 Cov.: 66 AF XY: 0.000184 AC XY: 110AN XY: 596320
GnomAD4 genome AF: 0.000374 AC: 57AN: 152216Hom.: 0 Cov.: 34 AF XY: 0.000322 AC XY: 24AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at