Variant chr2-5692502-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.693

Variant links:

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]

SOX11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 linkuse as main transcript	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 linkuse as main transcript	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.:

show subpopulations

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.:

AF XY:

0.103

AC XY:

7580

AN XY:

73588

show subpopulations

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.:

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

LINK: link

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

DANN

Benign

0.94

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over