12-65278787-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PM5BP4
The ENST00000355192.8(MSRB3):c.19C>T(p.Leu7Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000508 in 1,574,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L7R) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000355192.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSRB3 | NM_001031679.3 | c.-130C>T | 5_prime_UTR_variant | 1/7 | ENST00000308259.10 | NP_001026849.1 | ||
MSRB3 | NM_198080.4 | c.19C>T | p.Leu7Phe | missense_variant | 1/6 | NP_932346.1 | ||
MSRB3 | NM_001193460.2 | c.-294C>T | 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.-130C>T | 5_prime_UTR_variant | 1/7 | 1 | NM_001031679.3 | ENSP00000312274 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000492 AC: 7AN: 1422150Hom.: 0 Cov.: 31 AF XY: 0.00000284 AC XY: 2AN XY: 703646
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.19C>T (p.L7F) alteration is located in exon 1 (coding exon 1) of the MSRB3 gene. This alteration results from a C to T substitution at nucleotide position 19, causing the leucine (L) at amino acid position 7 to be replaced by a phenylalanine (F). 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