chr12-24236726-G-T

Position:

• chr12-24236726-G-T

Variant summary

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

The NM_152989.5(SOX5):​c.-2+40490C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,138 control chromosomes in the GnomAD database, including 47,771 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 0.78 (47771 hom., cov: 33)
• Consequence: SOX5 NM_152989.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX5	NM_152989.5	c.-2+40490C>A		intron_variant			NP_694534.1
SOX5	NM_001261414.3	c.-76-23309C>A		intron_variant			NP_001248343.1
SOX5	XM_011520835.3	c.-2+40490C>A		intron_variant			XP_011519137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX5	ENST00000646273.1	c.-76-23309C>A		intron_variant				ENSP00000493866.1
SOX5	ENST00000704300.1	c.-2+40490C>A		intron_variant				ENSP00000515824.1
SOX5	ENST00000536729.2	c.-76-23309C>A		intron_variant		5		ENSP00000496161.1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119283 AN: 152020 Hom.: 47714 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.785 AC: 119397 AN: 152138 Hom.: 47771 Cov.: 33 AF XY: 0.787 AC XY: 58513 AN XY: 74378

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.786

Alfa AF: 0.715 Hom.: 78036

Bravo AF: 0.793

Asia WGS AF: 0.850 AC: 2950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464500; hg19: chr12-24389660;