chr12-56164373-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000394023.7(SMARCC2):c.3317-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000191 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000394023.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCC2 | NM_001330288.2 | c.3591C>T | p.Ala1197= | synonymous_variant | 28/29 | ENST00000550164.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCC2 | ENST00000550164.6 | c.3591C>T | p.Ala1197= | synonymous_variant | 28/29 | 5 | NM_001330288.2 | A2 | |
ENST00000553176.1 | n.213-1824C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000221 AC: 55AN: 249218Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134874
GnomAD4 exome AF: 0.000177 AC: 259AN: 1461444Hom.: 0 Cov.: 32 AF XY: 0.000206 AC XY: 150AN XY: 726990
GnomAD4 genome AF: 0.000322 AC: 49AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74498
ClinVar
Submissions by phenotype
SMARCC2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | SMARCC2: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at