chr12-23601275-T-C

Position:

• chr12-23601275-T-C

Variant summary

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

The NM_006940.6(SOX5):​c.1164+3112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,980 control chromosomes in the GnomAD database, including 5,258 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 0.24 (5258 hom., cov: 30)
• Consequence: SOX5 NM_006940.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.84

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=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX5	NM_006940.6	c.1164+3112A>G		intron_variant		ENST00000451604.7	NP_008871.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX5	ENST00000451604.7	c.1164+3112A>G		intron_variant		1	NM_006940.6	ENSP00000398273	A1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36070 AN: 151860 Hom.: 5253 Cov.: 30

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.238 AC: 36107 AN: 151980 Hom.: 5258 Cov.: 30 AF XY: 0.234 AC XY: 17360 AN XY: 74286

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.222

Alfa AF: 0.179 Hom.: 4633

Bravo AF: 0.262

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	21
DANN	Benign	0.84

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: rs10771006; hg19: chr12-23754209;