chr9-2039776-ACAGCAGCAGCAGCAGCAGCAGCAG-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_003070.5(SMARCA2):c.684_707delGCAGCAGCAGCAGCAGCAGCAGCA(p.Gln229_Gln236del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,596,348 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_003070.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.684_707delGCAGCAGCAGCAGCAGCAGCAGCA | p.Gln229_Gln236del | disruptive_inframe_deletion | Exon 4 of 34 | ENST00000349721.8 | NP_003061.3 | |
SMARCA2 | NM_001289396.2 | c.684_707delGCAGCAGCAGCAGCAGCAGCAGCA | p.Gln229_Gln236del | disruptive_inframe_deletion | Exon 4 of 34 | NP_001276325.1 | ||
SMARCA2 | NM_139045.4 | c.684_707delGCAGCAGCAGCAGCAGCAGCAGCA | p.Gln229_Gln236del | disruptive_inframe_deletion | Exon 4 of 33 | NP_620614.2 | ||
SMARCA2 | NM_001289397.2 | c.684_707delGCAGCAGCAGCAGCAGCAGCAGCA | p.Gln229_Gln236del | disruptive_inframe_deletion | Exon 4 of 33 | NP_001276326.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000598 AC: 9AN: 150432Hom.: 0 Cov.: 26
GnomAD4 exome AF: 0.0000422 AC: 61AN: 1445816Hom.: 0 AF XY: 0.0000334 AC XY: 24AN XY: 718570
GnomAD4 genome AF: 0.0000598 AC: 9AN: 150532Hom.: 0 Cov.: 26 AF XY: 0.0000680 AC XY: 5AN XY: 73486
ClinVar
Submissions by phenotype
not specified Uncertain:1
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not provided Uncertain:1
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Inborn genetic diseases Benign:1
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