rs75990461
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001031679.3(MSRB3):c.293-6T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 1,611,986 control chromosomes in the GnomAD database, including 394 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001031679.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.293-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000308259.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRB3 | ENST00000308259.10 | c.293-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001031679.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0276 AC: 4196AN: 152142Hom.: 209 Cov.: 32
GnomAD3 exomes AF: 0.00733 AC: 1841AN: 251004Hom.: 97 AF XY: 0.00532 AC XY: 721AN XY: 135632
GnomAD4 exome AF: 0.00279 AC: 4070AN: 1459726Hom.: 184 Cov.: 30 AF XY: 0.00242 AC XY: 1760AN XY: 726334
GnomAD4 genome ? AF: 0.0276 AC: 4202AN: 152260Hom.: 210 Cov.: 32 AF XY: 0.0260 AC XY: 1939AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | 293-6T>C in Intron 06 of MSRB3: This variant is not expected to have clinical si gnificance because it has been identified in 9.4% (353/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs75990461). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at