12-24282487-T-C

Position:

• chr12-24282487-T-C

Variant summary

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

The NM_152989.5(SOX5):​c.-98-5175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 150,756 control chromosomes in the GnomAD database, including 38,205 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 0.70 (38205 hom., cov: 29)
• Consequence: SOX5 NM_152989.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

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]

SOX5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX5	NM_152989.5	c.-98-5175A>G		intron_variant			NP_694534.1
SOX5	NM_001261414.3	c.-173-5175A>G		intron_variant			NP_001248343.1
SOX5	XM_011520835.3	c.-98-5175A>G		intron_variant			XP_011519137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX5	ENST00000646273.1	c.-173-5175A>G		intron_variant				ENSP00000493866.1
SOX5	ENST00000704300.1	c.-98-5175A>G		intron_variant				ENSP00000515824.1
SOX5	ENST00000536729.2	c.-173-5175A>G		intron_variant		5		ENSP00000496161.1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 105567 AN: 150648 Hom.: 38197 Cov.: 29

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.701 AC: 105607 AN: 150756 Hom.: 38205 Cov.: 29 AF XY: 0.709 AC XY: 52180 AN XY: 73632

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.733

Alfa AF: 0.749 Hom.: 22714

Bravo AF: 0.689

Asia WGS AF: 0.844 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.055
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs526058; hg19: chr12-24435421;