chr12-56164613-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001330288.2(SMARCC2):c.3351G>A(p.Pro1117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,613,342 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 5 hom. )
Consequence
SMARCC2
NM_001330288.2 synonymous
NM_001330288.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.623
Genes affected
SMARCC2 (HGNC:11105): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2) The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and contains a predicted leucine zipper motif typical of many transcription factors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 12-56164613-C-T is Benign according to our data. Variant chr12-56164613-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1711343.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.623 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00153 (232/152106) while in subpopulation NFE AF= 0.00266 (181/67988). AF 95% confidence interval is 0.00234. There are 0 homozygotes in gnomad4. There are 110 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 232 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCC2 | NM_001330288.2 | c.3351G>A | p.Pro1117= | synonymous_variant | 28/29 | ENST00000550164.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCC2 | ENST00000550164.6 | c.3351G>A | p.Pro1117= | synonymous_variant | 28/29 | 5 | NM_001330288.2 | A2 | |
ENST00000553176.1 | n.213-2064G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00153 AC: 232AN: 151988Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00107 AC: 267AN: 249664Hom.: 0 AF XY: 0.00115 AC XY: 155AN XY: 135028
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GnomAD4 exome AF: 0.00176 AC: 2572AN: 1461236Hom.: 5 Cov.: 32 AF XY: 0.00177 AC XY: 1288AN XY: 726894
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GnomAD4 genome ? AF: 0.00153 AC: 232AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.00148 AC XY: 110AN XY: 74358
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | SMARCC2: BP4, BP7, BS1 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at