1-204100710-G-T

Variant names:

• chr1-204100710-G-T
• rs3795579
• NM_005686.3:c.-1-12205G>T

Variant summary

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

The NM_005686.3(SOX13):​c.-1-12205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,898 control chromosomes in the GnomAD database, including 9,702 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 0.36 (9702 hom., cov: 30)
• Consequence: SOX13 NM_005686.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX13	NM_005686.3	MANE Select	c.-1-12205G>T		intron	N/A	NP_005677.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX13	ENST00000367204.6	TSL:1 MANE Select	c.-1-12205G>T		intron	N/A	ENSP00000356172.1
	SOX13	ENST00000367203.8	TSL:1	n.598-12205G>T		intron	N/A
	SOX13	ENST00000528591.5	TSL:4	c.-1-12205G>T		intron	N/A	ENSP00000436297.1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53883 AN: 151778 Hom.: 9684 Cov.: 30

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.355 AC: 53941 AN: 151898 Hom.: 9702 Cov.: 30 AF XY: 0.355 AC XY: 26310 AN XY: 74216

African (AFR) AF: 0.340 AC: 14104 AN: 41438

American (AMR) AF: 0.421 AC: 6435 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1437 AN: 3462

East Asian (EAS) AF: 0.259 AC: 1337 AN: 5156

South Asian (SAS) AF: 0.459 AC: 2197 AN: 4790

European-Finnish (FIN) AF: 0.324 AC: 3417 AN: 10540

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23724 AN: 67920

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.353 Hom.: 30233

Bravo AF: 0.359

Asia WGS AF: 0.373 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.53
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3795579; hg19: chr1-204069838;