3-181712411-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003106.4(SOX2):āc.51T>Cā(p.Thr17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,441,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0 ( 0 hom., cov: 32)
Exomes š: 0.0000062 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SOX2
NM_003106.4 synonymous
NM_003106.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.119
Genes affected
SOX2 (HGNC:11195): (SRY-box transcription factor 2) This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT). [provided by RefSeq, Jul 2008]
SOX2-OT (HGNC:20209): (SOX2 overlapping transcript) This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]
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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=-0.55).
BP6
Variant 3-181712411-T-C is Benign according to our data. Variant chr3-181712411-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 750266.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX2 | NM_003106.4 | c.51T>C | p.Thr17= | synonymous_variant | 1/1 | ENST00000325404.3 | |
SOX2-OT | NR_075091.1 | n.783-2774T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX2 | ENST00000325404.3 | c.51T>C | p.Thr17= | synonymous_variant | 1/1 | NM_003106.4 | P1 | ||
SOX2-OT | ENST00000626948.3 | n.837-2774T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 149770Hom.: 0 Cov.: 32 FAILED QC
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GnomAD3 exomes AF: 0.00000949 AC: 2AN: 210642Hom.: 0 AF XY: 0.0000173 AC XY: 2AN XY: 115632
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GnomAD4 exome AF: 0.00000625 AC: 9AN: 1441098Hom.: 0 Cov.: 33 AF XY: 0.00000979 AC XY: 7AN XY: 715106
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 149770Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73136
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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 | Invitae | Jul 31, 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