rs297339

chr11-16382737-T-C

Variant summary

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

The ENST00000528429.5(SOX6):c.-5+20063A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,682 control chromosomes in the GnomAD database, including 35,815 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 0.69 (35815 hom., cov: 30)
• Consequence: SOX6 ENST00000528429.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX6	NM_001145811.2	c.-5+25961A>G		intron_variant
SOX6	NM_001145819.2	c.-5+20063A>G		intron_variant
SOX6	NM_001367872.1	c.-4-41485A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX6	ENST00000396356.7	c.-4-41485A>G		intron_variant		1		P4
SOX6	ENST00000527619.6	c.-5+19922A>G		intron_variant		1		A2
SOX6	ENST00000528429.5	c.-5+20063A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103858 AN: 151564 Hom.: 35777 Cov.: 30

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.685 AC: 103944 AN: 151682 Hom.: 35815 Cov.: 30 AF XY: 0.682 AC XY: 50530 AN XY: 74134

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.661

Alfa AF: 0.696 Hom.: 4890

Bravo AF: 0.680

Asia WGS AF: 0.519 AC: 1802 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs297339; hg19: chr11-16404283;