NM_003073.5:c.10_12delATG
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM1PM4_SupportingBP6BS2
The NM_003073.5(SMARCB1):c.10_12delATG(p.Met4del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000243 in 1,602,114 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003073.5 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCB1 | NM_003073.5 | c.10_12delATG | p.Met4del | conservative_inframe_deletion | Exon 1 of 9 | ENST00000644036.2 | NP_003064.2 | |
SMARCB1 | NM_001362877.2 | c.10_12delATG | p.Met4del | conservative_inframe_deletion | Exon 1 of 9 | NP_001349806.1 | ||
SMARCB1 | NM_001317946.2 | c.10_12delATG | p.Met4del | conservative_inframe_deletion | Exon 1 of 9 | NP_001304875.1 | ||
SMARCB1 | NM_001007468.3 | c.10_12delATG | p.Met4del | conservative_inframe_deletion | Exon 1 of 9 | NP_001007469.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151956Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000262 AC: 38AN: 1450158Hom.: 0 AF XY: 0.0000249 AC XY: 18AN XY: 721868
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151956Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74216
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 1 Uncertain:1
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not provided Uncertain:1
This variant, c.10_12del, results in the deletion of 1 amino acid(s) of the SMARCB1 protein (p.Met4del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SMARCB1-related conditions. ClinVar contains an entry for this variant (Variation ID: 532969). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as 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