rs7118395

Variant names:

• chr11-16177519-G-A
• rs7118395
• NM_001367873.1:c.777+6367C>T

Variant summary

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

The NM_001367873.1(SOX6):​c.777+6367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,636 control chromosomes in the GnomAD database, including 27,206 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 0.59 (27206 hom., cov: 31)
• Consequence: SOX6 NM_001367873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX6	NM_001367873.1	c.777+6367C>T		intron_variant	Intron 6 of 15	ENST00000683767.1	NP_001354802.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX6	ENST00000683767.1	c.777+6367C>T		intron_variant	Intron 6 of 15		NM_001367873.1	ENSP00000507545.1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89055 AN: 151516 Hom.: 27171 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.588 AC: 89146 AN: 151636 Hom.: 27206 Cov.: 31 AF XY: 0.591 AC XY: 43822 AN XY: 74118

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.599

Alfa AF: 0.544 Hom.: 3914

Bravo AF: 0.596

Asia WGS AF: 0.741 AC: 2570 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.47

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: rs7118395; hg19: chr11-16199065;