Genetic Variant NM_005686.3:c.776-14T>C (chr1-204121886-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005686.3(SOX13):c.776-14T>C variant causes a 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
NM_005686.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005686.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX13	NM_005686.3	MANE Select	c.776-14T>C		intron	N/A	NP_005677.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SOX13	ENST00000367204.6	TSL:1 MANE Select	c.776-14T>C	intron	N/A	ENSP00000356172.1	Q9UN79
SOX13	ENST00000618875.4	TSL:1	c.776-14T>C	intron	N/A	ENSP00000478239.1	Q9UN79
SOX13	ENST00000889805.1		c.809-14T>C	intron	N/A	ENSP00000559864.1

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

GnomAD2 exomes

AF:

0.0464

AC:

11457

AN:

246716

AF XY:

0.0442

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 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

African (AFR)

AF:

0.225

AC:

7438

AN:

33098

American (AMR)

AF:

0.0368

AC:

1642

AN:

44632

Ashkenazi Jewish (ASJ)

AF:

0.0552

AC:

1436

AN:

26014

East Asian (EAS)

AF:

0.000101

AC:

AN:

39626

South Asian (SAS)

AF:

0.0282

AC:

2418

AN:

85708

European-Finnish (FIN)

AF:

0.0149

AC:

795

AN:

53324

Middle Eastern (MID)

AF:

0.0704

AC:

405

AN:

5750

European-Non Finnish (NFE)

AF:

0.0456

AC:

50036

AN:

1097586

Other (OTH)

AF:

0.0525

AC:

3143

AN:

59828

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

2795

5589

8384

11178

13973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1914

3828

5742

7656

9570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0893

AC:

13583

AN:

152190

Hom.:

1055

Cov.:

AF XY:

0.0857

AC XY:

6381

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.213

AC:

8835

AN:

41468

American (AMR)

AF:

0.0601

AC:

920

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0571

AC:

198

AN:

3470

East Asian (EAS)

AF:

0.000579

AC:

AN:

5180

South Asian (SAS)

AF:

0.0261

AC:

126

AN:

4830

European-Finnish (FIN)

AF:

0.0161

AC:

171

AN:

10622

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0457

AC:

3107

AN:

67994

Other (OTH)

AF:

0.0922

AC:

195

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

589

1177

1766

2354

2943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0568

Hom.:

323

Bravo

AF:

0.0994

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.97

PhyloP100

-0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over