12-65278850-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000355192.8(MSRB3):āc.82G>Cā(p.Gly28Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000896 in 1,562,098 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000355192.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.-67G>C | 5_prime_UTR_variant | 1/7 | ENST00000308259.10 | NP_001026849.1 | ||
MSRB3 | NM_198080.4 | c.82G>C | p.Gly28Arg | missense_variant | 1/6 | NP_932346.1 | ||
MSRB3 | NM_001193460.2 | c.-231G>C | 5_prime_UTR_variant | 1/8 | NP_001180389.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSRB3 | ENST00000308259.10 | c.-67G>C | 5_prime_UTR_variant | 1/7 | 1 | NM_001031679.3 | ENSP00000312274 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000401 AC: 67AN: 166970Hom.: 0 AF XY: 0.000384 AC XY: 34AN XY: 88432
GnomAD4 exome AF: 0.0000816 AC: 115AN: 1409878Hom.: 2 Cov.: 31 AF XY: 0.0000833 AC XY: 58AN XY: 696350
GnomAD4 genome AF: 0.000164 AC: 25AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74410
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 05, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 11, 2023 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.82G>C (p.G28R) alteration is located in exon 1 (coding exon 1) of the MSRB3 gene. This alteration results from a G to C substitution at nucleotide position 82, causing the glycine (G) at amino acid position 28 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 22, 2017 | proposed classification - variant undergoing re-assessment, contact laboratory - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at