Variant 20-64049125-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018419.3(SOX18):c.358+34A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 1594 hom., cov: 14)

Exomes 𝑓: 0.24 ( 8721 hom. )

Consequence

SOX18
NM_018419.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.755

Variant links:

Genes affected

SOX18 (HGNC:11194): (SRY-box transcription factor 18) 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. This protein plays a role in hair, blood vessel, and lymphatic vessel development. Mutations in this gene have been associated with recessive and dominant forms of hypotrichosis-lymphedema-telangiectasia. [provided by RefSeq, Jul 2008]

SOX18 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 20-64049125-T-G is Benign according to our data. Variant chr20-64049125-T-G is described in ClinVar as [Benign]. Clinvar id is 261030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX18	NM_018419.3 linkuse as main transcript	c.358+34A>C		intron_variant		ENST00000340356.9	NP_060889.1	P35713

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX18	ENST00000340356.9 linkuse as main transcript	c.358+34A>C		intron_variant		1	NM_018419.3	ENSP00000341815.7		P35713

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

20285

AN:

67006

Hom.:

1592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.286

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.284

GnomAD3 exomes

AF:

0.205

AC:

15495

AN:

75552

Hom.:

1262

AF XY:

0.213

AC XY:

9596

AN XY:

45050

show subpopulations

Gnomad AFR exome

AF:

0.207

Gnomad AMR exome

AF:

0.198

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.0591

Gnomad SAS exome

AF:

0.366

Gnomad FIN exome

AF:

0.174

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.237

AC:

129733

AN:

547650

Hom.:

8721

Cov.:

AF XY:

0.237

AC XY:

65825

AN XY:

277312

show subpopulations

Gnomad4 AFR exome

AF:

0.311

Gnomad4 AMR exome

AF:

0.132

Gnomad4 ASJ exome

AF:

0.249

Gnomad4 EAS exome

AF:

0.0959

Gnomad4 SAS exome

AF:

0.334

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.251

GnomAD4 genome

AF:

0.303

AC:

20300

AN:

67046

Hom.:

1594

Cov.:

AF XY:

0.307

AC XY:

10043

AN XY:

32744

show subpopulations

Gnomad4 AFR

AF:

0.368

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.122

Gnomad4 SAS

AF:

0.471

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.265

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.0521

Hom.:

Asia WGS

AF:

0.171

AC:

513

AN:

3018

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.61

DANN

Benign

0.41

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over