rs12576205

Positions:

• chr11-16009017-G-A
• chr11-16009017-G-T

Variant summary

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

The NM_001367873.1(SOX6):​c.1732+5925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 151,916 control chromosomes in the GnomAD database, including 1,276 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 0.090 (1276 hom., cov: 32)
• Consequence: SOX6 NM_001367873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX6	NM_001367873.1	c.1732+5925C>T		intron_variant		ENST00000683767.1	NP_001354802.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX6	ENST00000683767.1	c.1732+5925C>T		intron_variant			NM_001367873.1	ENSP00000507545	A2

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13659 AN: 151796 Hom.: 1271 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00918

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0901 AC: 13682 AN: 151916 Hom.: 1276 Cov.: 32 AF XY: 0.0942 AC XY: 6992 AN XY: 74228

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.00919

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0565 Hom.: 85

Bravo AF: 0.104

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.62

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: rs12576205; hg19: chr11-16030563;