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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_003070.5(SMARCA2):c.690_707del(p.Gln233_Gln238del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,596,344 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). 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 Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.690_707del | p.Gln233_Gln238del | inframe_deletion | 4/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.690_707del | p.Gln233_Gln238del | inframe_deletion | 4/34 | ||
SMARCA2 | NM_001289397.2 | c.690_707del | p.Gln233_Gln238del | inframe_deletion | 4/33 | ||
SMARCA2 | NM_139045.4 | c.690_707del | p.Gln233_Gln238del | inframe_deletion | 4/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.690_707del | p.Gln233_Gln238del | inframe_deletion | 4/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000312 AC: 47AN: 150432Hom.: 0 Cov.: 26
GnomAD4 exome AF: 0.000136 AC: 197AN: 1445812Hom.: 0 AF XY: 0.000132 AC XY: 95AN XY: 718568
GnomAD4 genome AF: 0.000312 AC: 47AN: 150532Hom.: 0 Cov.: 26 AF XY: 0.000381 AC XY: 28AN XY: 73486
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | SMARCA2: BS1 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | This variant is not present in population databases (gnomAD no frequency). This variant, c.690_707del, results in the deletion of 6 amino acid(s) of the SMARCA2 protein (p.Gln233_Gln238del), but otherwise preserves the integrity of the reading frame. This variant has not been reported in the literature in individuals affected with SMARCA2-related conditions. 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at