rs1155685

Variant names:

• chr11-16293703-C-A
• rs1155685
• NM_001367873.1:c.445+24743G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-16293703-C-A
• chr11-16293703-C-G

Variant summary

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

The NM_001367873.1(SOX6):​c.445+24743G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,000 control chromosomes in the GnomAD database, including 46,487 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 (46487 hom., cov: 31)
• Consequence: SOX6 NM_001367873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX6	NM_001367873.1	c.445+24743G>T		intron_variant	Intron 3 of 15	ENST00000683767.1	NP_001354802.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX6	ENST00000683767.1	c.445+24743G>T		intron_variant	Intron 3 of 15		NM_001367873.1	ENSP00000507545.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118619 AN: 151882 Hom.: 46452 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.781 AC: 118706 AN: 152000 Hom.: 46487 Cov.: 31 AF XY: 0.783 AC XY: 58166 AN XY: 74292

African (AFR) AF: 0.764 AC: 31687 AN: 41452

American (AMR) AF: 0.689 AC: 10486 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2840 AN: 3466

East Asian (EAS) AF: 0.760 AC: 3918 AN: 5154

South Asian (SAS) AF: 0.765 AC: 3684 AN: 4816

European-Finnish (FIN) AF: 0.866 AC: 9178 AN: 10598

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54298 AN: 67974

Other (OTH) AF: 0.794 AC: 1673 AN: 2106

Alfa AF: 0.762 Hom.: 2615

Bravo AF: 0.766

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.1
DANN	Benign	0.56
PhyloP100		0.17
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: rs1155685; hg19: chr11-16315249;