chr22-41866943-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004599.4(SREBF2):āc.201T>Cā(p.Ser67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000415 in 1,613,522 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0024 ( 2 hom., cov: 32)
Exomes š: 0.00021 ( 2 hom. )
Consequence
SREBF2
NM_004599.4 synonymous
NM_004599.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.560
Genes affected
SREBF2 (HGNC:11290): (sterol regulatory element binding transcription factor 2) This gene encodes a member of the a ubiquitously expressed transcription factor that controls cholesterol homeostasis by regulating transcription of sterol-regulated genes. The encoded protein contains a basic helix-loop-helix-leucine zipper (bHLH-Zip) domain and binds the sterol regulatory element 1 motif. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 22-41866943-T-C is Benign according to our data. Variant chr22-41866943-T-C is described in ClinVar as [Benign]. Clinvar id is 786383.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.56 with no splicing effect.
BS2
High AC in GnomAd4 at 359 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SREBF2 | NM_004599.4 | c.201T>C | p.Ser67= | synonymous_variant | 2/19 | ENST00000361204.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SREBF2 | ENST00000361204.9 | c.201T>C | p.Ser67= | synonymous_variant | 2/19 | 1 | NM_004599.4 | P3 | |
SREBF2 | ENST00000424354.5 | c.201T>C | p.Ser67= | synonymous_variant, NMD_transcript_variant | 2/22 | 1 | |||
SREBF2 | ENST00000710853.1 | c.111T>C | p.Ser37= | synonymous_variant | 2/19 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00235 AC: 357AN: 151986Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000551 AC: 137AN: 248858Hom.: 1 AF XY: 0.000364 AC XY: 49AN XY: 134738
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GnomAD4 exome AF: 0.000212 AC: 310AN: 1461418Hom.: 2 Cov.: 32 AF XY: 0.000194 AC XY: 141AN XY: 727004
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GnomAD4 genome AF: 0.00236 AC: 359AN: 152104Hom.: 2 Cov.: 32 AF XY: 0.00204 AC XY: 152AN XY: 74356
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at