chr20-326560-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006943.4(SOX12):āc.636C>Gā(p.Ala212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000701 in 1,487,518 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 Benign (ā ).
Frequency
Genomes: š 0.0038 ( 4 hom., cov: 32)
Exomes š: 0.00035 ( 1 hom. )
Consequence
SOX12
NM_006943.4 synonymous
NM_006943.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.426
Genes affected
SOX12 (HGNC:11198): (SRY-box transcription factor 12) Members of the SOX family of transcription factors are characterized by the presence of a DNA-binding high mobility group (HMG) domain, homologous to the HMG box of sex-determining region Y (SRY). Forming a subgroup of the HMG domain superfamily, SOX proteins have been implicated in cell fate decisions in a diverse range of developmental processes. SOX transcription factors have diverse tissue-specific expression patterns during early development and have been proposed to act as target-specific transcription factors and/or as chromatin structure regulatory elements. The protein encoded by this gene was identified as a SOX family member based on conserved domains, and its expression in various tissues suggests a role in both differentiation and maintenance of several cell types. [provided by RefSeq, Jan 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=-0.62).
BP6
Variant 20-326560-C-G is Benign according to our data. Variant chr20-326560-C-G is described in ClinVar as [Benign]. Clinvar id is 734216.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.426 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX12 | NM_006943.4 | c.636C>G | p.Ala212= | synonymous_variant | 1/1 | ENST00000342665.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX12 | ENST00000342665.5 | c.636C>G | p.Ala212= | synonymous_variant | 1/1 | NM_006943.4 | P1 | ||
NRSN2-AS1 | ENST00000662580.1 | n.221-3995G>C | intron_variant, non_coding_transcript_variant | ||||||
NRSN2-AS1 | ENST00000442637.2 | n.126-3995G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00379 AC: 576AN: 151950Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.000642 AC: 64AN: 99638Hom.: 0 AF XY: 0.000576 AC XY: 32AN XY: 55520
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GnomAD4 exome AF: 0.000350 AC: 467AN: 1335458Hom.: 1 Cov.: 32 AF XY: 0.000331 AC XY: 218AN XY: 658368
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GnomAD4 genome AF: 0.00379 AC: 576AN: 152060Hom.: 4 Cov.: 32 AF XY: 0.00366 AC XY: 272AN 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 | Feb 09, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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