22-23836864-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003073.5(SMARCB1):c.*2684G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,459,896 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0025 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0036 ( 16 hom. )
Consequence
SMARCB1
NM_003073.5 3_prime_UTR
NM_003073.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.171
Genes affected
SMARCB1 (HGNC:11103): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1) The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing the transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and mutations in it have been associated with malignant rhabdoid tumors. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]
DERL3 (HGNC:14236): (derlin 3) The protein encoded by this gene belongs to the derlin family, and resides in the endoplasmic reticulum (ER). Proteins that are unfolded or misfolded in the ER must be refolded or degraded to maintain the homeostasis of the ER. This protein appears to be involved in the degradation of misfolded glycoproteins in the ER. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 22-23836864-G-A is Benign according to our data. Variant chr22-23836864-G-A is described in ClinVar as [Benign]. Clinvar id is 1711548.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 382 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00250 AC: 381AN: 152168Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00271 AC: 216AN: 79632Hom.: 2 AF XY: 0.00270 AC XY: 106AN XY: 39260
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GnomAD4 exome AF: 0.00360 AC: 4709AN: 1307610Hom.: 16 Cov.: 35 AF XY: 0.00368 AC XY: 2339AN XY: 635422
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GnomAD4 genome AF: 0.00251 AC: 382AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.00239 AC XY: 178AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | SMARCB1: BS1, BS2 - |
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at