rs1065024

Variant names:

• chr11-15967804-A-G
• rs1065024
• NM_001367873.1:c.*5005T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367873.1(SOX6):​c.*5005T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,944 control chromosomes in the GnomAD database, including 7,129 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 0.26 (7129 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: SOX6 NM_001367873.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 7 publications found

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]

SOX6 Gene-Disease associations (from GenCC):

• Tolchin-Le Caignec syndrome

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia, G2P, Illumina

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX6	NM_001367873.1	c.*5005T>C		3_prime_UTR_variant	Exon 16 of 16	ENST00000683767.1	NP_001354802.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX6	ENST00000683767.1	c.*5005T>C		3_prime_UTR_variant	Exon 16 of 16		NM_001367873.1	ENSP00000507545.1
SOX6	ENST00000396356.7	c.*5005T>C		3_prime_UTR_variant	Exon 16 of 16	1		ENSP00000379644.3
SOX6	ENST00000316399.10	c.*5005T>C		3_prime_UTR_variant	Exon 15 of 15	5		ENSP00000324948.6
SOX6	ENST00000655819.1	c.*5005T>C		3_prime_UTR_variant	Exon 15 of 15			ENSP00000499737.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38739 AN: 151816 Hom.: 7103 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.255 AC: 38808 AN: 151936 Hom.: 7129 Cov.: 32 AF XY: 0.255 AC XY: 18974 AN XY: 74272

African (AFR) AF: 0.506 AC: 20912 AN: 41358

American (AMR) AF: 0.231 AC: 3524 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2598 AN: 5120

South Asian (SAS) AF: 0.179 AC: 862 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10584

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8400 AN: 68004

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.172 Hom.: 4552

Bravo AF: 0.279

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.6
DANN	Benign	0.68
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1065024; hg19: chr11-15989350;