10-23104237-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_012228.4(MSRB2):c.212C>T(p.Thr71Met) variant causes a missense change. The variant allele was found at a frequency of 0.000054 in 1,612,372 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 (★).
Frequency
Consequence
NM_012228.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSRB2 | ENST00000376510.8 | c.212C>T | p.Thr71Met | missense_variant | Exon 2 of 5 | 1 | NM_012228.4 | ENSP00000365693.3 | ||
MSRB2 | ENST00000472663.1 | n.92C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000434990.1 | ||||
ENSG00000286924 | ENST00000655462.1 | n.116+29452G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000444 AC: 11AN: 247672Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134472
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460216Hom.: 0 Cov.: 30 AF XY: 0.0000427 AC XY: 31AN XY: 726498
GnomAD4 genome AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.212C>T (p.T71M) alteration is located in exon 2 (coding exon 2) of the MSRB2 gene. This alteration results from a C to T substitution at nucleotide position 212, causing the threonine (T) at amino acid position 71 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