rs11047102

chr12-23793212-C-T

Variant summary

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

The NM_006940.6(SOX5):c.482-37488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 152,066 control chromosomes in the GnomAD database, including 603 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 0.079 (603 hom., cov: 31)
• Consequence: SOX5 NM_006940.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

SOX5 (HGNC:11201): (SRY-box transcription factor 5) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX5	NM_006940.6	c.482-37488G>A		intron_variant		ENST00000451604.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX5	ENST00000451604.7	c.482-37488G>A		intron_variant		1	NM_006940.6	A1

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 12014 AN: 151948 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0790 AC: 12017 AN: 152066 Hom.: 603 Cov.: 31 AF XY: 0.0782 AC XY: 5813 AN XY: 74320

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.102 Hom.: 521

Bravo AF: 0.0810

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
Dann	Benign	0.39

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: rs11047102; hg19: chr12-23946146;