22-23834171-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003073.5(SMARCB1):c.1149G>A(p.Pro383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000833 in 1,439,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P383P) has been classified as Likely benign.
Frequency
Consequence
NM_003073.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCB1 | NM_003073.5 | c.1149G>A | p.Pro383= | synonymous_variant | 9/9 | ENST00000644036.2 | |
SMARCB1 | NM_001362877.2 | c.1203G>A | p.Pro401= | synonymous_variant | 9/9 | ||
SMARCB1 | NM_001317946.2 | c.1176G>A | p.Pro392= | synonymous_variant | 9/9 | ||
SMARCB1 | NM_001007468.3 | c.1122G>A | p.Pro374= | synonymous_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCB1 | ENST00000644036.2 | c.1149G>A | p.Pro383= | synonymous_variant | 9/9 | NM_003073.5 | A1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000473 AC: 1AN: 211458Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 114360
GnomAD4 exome AF: 0.00000833 AC: 12AN: 1439958Hom.: 0 Cov.: 33 AF XY: 0.0000112 AC XY: 8AN XY: 714396
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at