chr1-204102229-C-T

Position:

• chr1-204102229-C-T

Variant summary

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

The NM_005686.3(SOX13):​c.-1-10686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,246 control chromosomes in the GnomAD database, including 54,244 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 0.84 (54244 hom., cov: 33)
• Consequence: SOX13 NM_005686.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX13	NM_005686.3	c.-1-10686C>T		intron_variant		ENST00000367204.6	NP_005677.2
SOX13	XM_005245623.4	c.-1-10686C>T		intron_variant			XP_005245680.1
SOX13	XM_047435006.1	c.-1-10686C>T		intron_variant			XP_047290962.1
SOX13	XM_047435007.1	c.-1-10686C>T		intron_variant			XP_047290963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX13	ENST00000367204.6	c.-1-10686C>T		intron_variant		1	NM_005686.3	ENSP00000356172	P1

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128245 AN: 152128 Hom.: 54194 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.843 AC: 128352 AN: 152246 Hom.: 54244 Cov.: 33 AF XY: 0.842 AC XY: 62692 AN XY: 74428

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.868

Alfa AF: 0.843 Hom.: 24909

Bravo AF: 0.848

Asia WGS AF: 0.794 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs16776; hg19: chr1-204071357;