NM_152989.5:c.-98-14516G>A

Variant names:

• chr12-24291828-C-T
• rs12371851
• NM_152989.5:c.-98-14516G>A

Variant summary

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

The NM_152989.5(SOX5):​c.-98-14516G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,182 control chromosomes in the GnomAD database, including 1,694 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 0.13 (1694 hom., cov: 32)
• Consequence: SOX5 NM_152989.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 2 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 Gene-Disease associations (from GenCC):

• Lamb-Shaffer syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
• developmental and speech delay due to SOX5 deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX5	NM_152989.5	c.-98-14516G>A		intron_variant	Intron 3 of 17		NP_694534.1
SOX5	NM_001261414.3	c.-173-14516G>A		intron_variant	Intron 3 of 16		NP_001248343.1
SOX5	XM_011520835.3	c.-98-14516G>A		intron_variant	Intron 3 of 17		XP_011519137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX5	ENST00000646273.1	c.-173-14516G>A		intron_variant	Intron 3 of 16			ENSP00000493866.1
SOX5	ENST00000704300.1	c.-98-14516G>A		intron_variant	Intron 3 of 7			ENSP00000515824.1
SOX5	ENST00000536729.2	c.-173-14516G>A		intron_variant	Intron 1 of 4	5		ENSP00000496161.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19651 AN: 152064 Hom.: 1693 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.129 AC: 19652 AN: 152182 Hom.: 1694 Cov.: 32 AF XY: 0.128 AC XY: 9516 AN XY: 74402

African (AFR) AF: 0.0337 AC: 1398 AN: 41536

American (AMR) AF: 0.133 AC: 2036 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.107 AC: 517 AN: 4832

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10578

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12966 AN: 67994

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.168 Hom.: 2598

Bravo AF: 0.119

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.64
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12371851; hg19: chr12-24444762;