chr2-5692574-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003108.4(SOX11):c.-148G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0232 in 649,534 control chromosomes in the GnomAD database, including 241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.019 ( 37 hom., cov: 30)
Exomes 𝑓: 0.024 ( 204 hom. )
Consequence
SOX11
NM_003108.4 5_prime_UTR
NM_003108.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.35
Genes affected
SOX11 (HGNC:11191): (SRY-box transcription factor 11) This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The protein may function in the developing nervous system and play a role in tumorigenesis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 2-5692574-G-C is Benign according to our data. Variant chr2-5692574-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1210901.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0192 (2915/151748) while in subpopulation NFE AF= 0.0292 (1979/67816). AF 95% confidence interval is 0.0281. There are 37 homozygotes in gnomad4. There are 1367 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2916 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX11 | NM_003108.4 | c.-148G>C | 5_prime_UTR_variant | 1/1 | ENST00000322002.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX11 | ENST00000322002.5 | c.-148G>C | 5_prime_UTR_variant | 1/1 | NM_003108.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0192 AC: 2916AN: 151640Hom.: 37 Cov.: 30
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GnomAD4 exome AF: 0.0244 AC: 12170AN: 497786Hom.: 204 AF XY: 0.0236 AC XY: 6081AN XY: 257920
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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 | GeneDx | Oct 07, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at