chr9-2039776-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_003070.5(SMARCA2):βc.678_707delβ(p.Gln229_Gln238del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 150,532 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (β ). Synonymous variant affecting the same amino acid position (i.e. Q223Q) has been classified as Likely benign.
Frequency
Consequence
NM_003070.5 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.678_707del | p.Gln229_Gln238del | inframe_deletion | 4/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.678_707del | p.Gln229_Gln238del | inframe_deletion | 4/34 | ||
SMARCA2 | NM_001289397.2 | c.678_707del | p.Gln229_Gln238del | inframe_deletion | 4/33 | ||
SMARCA2 | NM_139045.4 | c.678_707del | p.Gln229_Gln238del | inframe_deletion | 4/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.678_707del | p.Gln229_Gln238del | inframe_deletion | 4/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000332 AC: 5AN: 150432Hom.: 0 Cov.: 26
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000885 AC: 128AN: 1445816Hom.: 0 AF XY: 0.0000738 AC XY: 53AN XY: 718568
GnomAD4 genome AF: 0.0000266 AC: 4AN: 150532Hom.: 0 Cov.: 26 AF XY: 0.0000272 AC XY: 2AN XY: 73486
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at