10-23104176-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012228.4(MSRB2):c.151A>G(p.Lys51Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSRB2 | NM_012228.4 | c.151A>G | p.Lys51Glu | missense_variant | 2/5 | ENST00000376510.8 | |
MSRB2 | XM_011519426.3 | c.151A>G | p.Lys51Glu | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRB2 | ENST00000376510.8 | c.151A>G | p.Lys51Glu | missense_variant | 2/5 | 1 | NM_012228.4 | P1 | |
ENST00000655462.1 | n.116+29513T>C | intron_variant, non_coding_transcript_variant | |||||||
MSRB2 | ENST00000472663.1 | c.34A>G | p.Lys12Glu | missense_variant, NMD_transcript_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249222Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135238
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727176
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.151A>G (p.K51E) alteration is located in exon 2 (coding exon 2) of the MSRB2 gene. This alteration results from a A to G substitution at nucleotide position 151, causing the lysine (K) at amino acid position 51 to be replaced by a glutamic acid (E). 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