rs760850788
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_001382264.1(MSRB1):c.172+1G>T variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001382264.1 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB1 | NM_016332.4 | c.173G>T | p.Arg58Leu | missense_variant | Exon 2 of 4 | ENST00000361871.8 | NP_057416.1 | |
MSRB1 | NM_001382265.1 | c.173G>T | p.Arg58Leu | missense_variant | Exon 2 of 3 | NP_001369194.1 | ||
MSRB1 | NM_001382264.1 | c.172+1G>T | splice_donor_variant, intron_variant | Intron 2 of 3 | NP_001369193.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461666Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727132
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.