Variant rs12089381 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000367204.6(SOX13):c.776-14T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 1,597,756 control chromosomes in the GnomAD database, including 3,268 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 0.089 ( 1055 hom., cov: 32)

Exomes 𝑓: 0.047 ( 2213 hom. )

Consequence

SOX13
ENST00000367204.6 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Variant links:

Genes affected

SOX13 (HGNC:11192): (SRY-box transcription factor 13) 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 cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. It has also been determined to be a type-1 diabetes autoantigen, also known as islet cell antibody 12. [provided by RefSeq, Jul 2008]

SOX13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SOX13	NM_005686.3 linkuse as main transcript	c.776-14T>C	splice_polypyrimidine_tract_variant, intron_variant	ENST00000367204.6	NP_005677.2
SOX13	XM_005245623.4 linkuse as main transcript	c.773-14T>C	splice_polypyrimidine_tract_variant, intron_variant		XP_005245680.1
SOX13	XM_047435006.1 linkuse as main transcript	c.776-14T>C	splice_polypyrimidine_tract_variant, intron_variant		XP_047290962.1
SOX13	XM_047435007.1 linkuse as main transcript	c.773-14T>C	splice_polypyrimidine_tract_variant, intron_variant		XP_047290963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
SOX13	ENST00000367204.6 linkuse as main transcript	c.776-14T>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_005686.3	ENSP00000356172	P1
SOX13	ENST00000618875.4 linkuse as main transcript	c.776-14T>C		splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000478239	P1
SOX13	ENST00000480326.1 linkuse as main transcript	c.374T>C	p.Leu125Pro	missense_variant, NMD_transcript_variant	4/6	5		ENSP00000434093
SOX13	ENST00000272193.10 linkuse as main transcript	n.643-14T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0891

AC:

13557

AN:

152072

Hom.:

1054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0602

Gnomad ASJ

AF:

0.0571

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0261

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0457

Gnomad OTH

AF:

0.0932

GnomAD3 exomes

AF:

0.0464

AC:

11457

AN:

246716

Hom.:

494

AF XY:

0.0442

AC XY:

5921

AN XY:

134054

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.0343

Gnomad ASJ exome

AF:

0.0589

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0269

Gnomad FIN exome

AF:

0.0140

Gnomad NFE exome

AF:

0.0454

Gnomad OTH exome

AF:

0.0461

GnomAD4 exome

AF:

0.0466

AC:

67317

AN:

1445566

Hom.:

2213

Cov.:

AF XY:

0.0456

AC XY:

32845

AN XY:

720064

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.0368

Gnomad4 ASJ exome

AF:

0.0552

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0282

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.0456

Gnomad4 OTH exome

AF:

0.0525

GnomAD4 genome

AF:

0.0893

AC:

13583

AN:

152190

Hom.:

1055

Cov.:

AF XY:

0.0857

AC XY:

6381

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.0601

Gnomad4 ASJ

AF:

0.0571

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0261

Gnomad4 FIN

AF:

0.0161

Gnomad4 NFE

AF:

0.0457

Gnomad4 OTH

AF:

0.0922

Alfa

AF:

0.0576

Hom.:

162

Bravo

AF:

0.0994

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.97

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over