rs1464502

Variant names:

• chr12-24235155-A-G
• rs1464502
• NM_152989.5:c.-2+42061T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152989.5(SOX5):​c.-2+42061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,120 control chromosomes in the GnomAD database, including 8,059 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 0.32 (8059 hom., cov: 33)
• Consequence: SOX5 NM_152989.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

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:53311): (SOX5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX5	NM_152989.5	c.-2+42061T>C		intron_variant	Intron 4 of 17		NP_694534.1
SOX5	NM_001261414.3	c.-76-21738T>C		intron_variant	Intron 4 of 16		NP_001248343.1
SOX5-AS1	NR_120472.1	n.446-2667A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX5	ENST00000646273.1	c.-76-21738T>C		intron_variant	Intron 4 of 16			ENSP00000493866.1
SOX5	ENST00000704300.1	c.-2+42061T>C		intron_variant	Intron 4 of 7			ENSP00000515824.1
SOX5	ENST00000536729.2	c.-76-21738T>C		intron_variant	Intron 2 of 4	5		ENSP00000496161.1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48120 AN: 152002 Hom.: 8035 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.317 AC: 48186 AN: 152120 Hom.: 8059 Cov.: 33 AF XY: 0.312 AC XY: 23203 AN XY: 74352

African (AFR) AF: 0.384 AC: 15939 AN: 41476

American (AMR) AF: 0.264 AC: 4041 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.0786 AC: 407 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2889 AN: 10576

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22015 AN: 67986

Other (OTH) AF: 0.307 AC: 650 AN: 2116

Alfa AF: 0.323 Hom.: 6007

Bravo AF: 0.316

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs1464502; hg19: chr12-24388089;