rs10766295

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001367873.1(SOX6):​c.1101+12152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,052 control chromosomes in the GnomAD database, including 8,775 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8775 hom., cov: 32)

Consequence

SOX6
NM_001367873.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.485
Variant links:
Genes affected
SOX6 (HGNC:16421): (SRY-box transcription factor 6) This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SOX6NM_001367873.1 linkuse as main transcriptc.1101+12152A>G intron_variant ENST00000683767.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SOX6ENST00000683767.1 linkuse as main transcriptc.1101+12152A>G intron_variant NM_001367873.1 A2P35712-1

Frequencies

GnomAD3 genomes
AF:
0.310
AC:
47062
AN:
151934
Hom.:
8776
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0985
Gnomad AMI
AF:
0.411
Gnomad AMR
AF:
0.393
Gnomad ASJ
AF:
0.258
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.395
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.414
Gnomad OTH
AF:
0.298
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.310
AC:
47069
AN:
152052
Hom.:
8775
Cov.:
32
AF XY:
0.309
AC XY:
22983
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.0983
Gnomad4 AMR
AF:
0.394
Gnomad4 ASJ
AF:
0.258
Gnomad4 EAS
AF:
0.238
Gnomad4 SAS
AF:
0.306
Gnomad4 FIN
AF:
0.395
Gnomad4 NFE
AF:
0.414
Gnomad4 OTH
AF:
0.293
Alfa
AF:
0.387
Hom.:
22870
Bravo
AF:
0.298
Asia WGS
AF:
0.236
AC:
822
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.6
DANN
Benign
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs10766295; hg19: chr11-16105390; API