2-5692502-C-A

Position:

• chr2-5692502-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003108.4(SOX11):​c.-220C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 150,674 control chromosomes in the GnomAD database, including 983 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (983 hom., cov: 31)
• Consequence: SOX11 NM_003108.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.693

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant 2-5692502-C-A is Benign according to our data. Variant chr2-5692502-C-A is described in ClinVar as [Benign]. Clinvar id is 1270826.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX11	NM_003108.4	c.-220C>A		5_prime_UTR_variant	1/1	ENST00000322002.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX11	ENST00000322002.5	c.-220C>A		5_prime_UTR_variant	1/1		NM_003108.4	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15470 AN: 150568 Hom.: 983 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00159

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0677

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.103 AC: 15481 AN: 150674 Hom.: 983 Cov.: 31 AF XY: 0.103 AC XY: 7580 AN XY: 73588

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00159

Gnomad4 SAS AF: 0.0850

Gnomad4 FIN AF: 0.0708

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0342 Hom.: 23

Bravo AF: 0.115

Asia WGS AF: 0.0520 AC: 182 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs183761758; hg19: chr2-5832634;