11-16258758-A-T

Position:

• chr11-16258758-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367873.1(SOX6):​c.446-24087T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 151,558 control chromosomes in the GnomAD database, including 46,501 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 0.78 (46501 hom., cov: 29)
• Consequence: SOX6 NM_001367873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX6	NM_001367873.1	c.446-24087T>A		intron_variant		ENST00000683767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX6	ENST00000683767.1	c.446-24087T>A		intron_variant			NM_001367873.1	A2

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118470 AN: 151440 Hom.: 46474 Cov.: 29

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.782 AC: 118547 AN: 151558 Hom.: 46501 Cov.: 29 AF XY: 0.784 AC XY: 58054 AN XY: 74056

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.798

Alfa AF: 0.802 Hom.: 6087

Bravo AF: 0.768

Asia WGS AF: 0.805 AC: 2795 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.89

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

Other links and lift over

dbSNP: rs10832576; hg19: chr11-16280304;