Variant 13-36191833-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_017826.3(SOHLH2):c.492C>T(p.Ser164=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00991 in 1,613,844 control chromosomes in the GnomAD database, including 274 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 84 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 190 hom. )

Consequence

SOHLH2
NM_017826.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0220

Variant links:

Genes affected

SOHLH2 (HGNC:26026): (spermatogenesis and oogenesis specific basic helix-loop-helix 2) This gene encodes one of testis-specific transcription factors which are essential for spermatogenesis, oogenesis and folliculogenesis. This gene is located on chromosome 13. The proteins encoded by this gene and another testis-specific transcription factor, SOHLH1, can form heterodimers, in addition to homodimers. There is a read-through locus (GeneID: 100526761) that shares sequence identity with this gene and the upstream CCDC169 (GeneID: 728591). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

SOHLH2 links:

CCDC169-SOHLH2 (HGNC:):

CCDC169-SOHLH2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 13-36191833-G-A is Benign according to our data. Variant chr13-36191833-G-A is described in ClinVar as [Benign]. Clinvar id is 3037375.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.022 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.061 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SOHLH2	NM_017826.3 linkuse as main transcript	c.492C>T	p.Ser164=	synonymous_variant	5/11	ENST00000379881.8
CCDC169-SOHLH2	NM_001198910.2 linkuse as main transcript	c.723C>T	p.Ser241=	synonymous_variant	10/16
SOHLH2	NM_001282147.2 linkuse as main transcript	c.492C>T	p.Ser164=	synonymous_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOHLH2	ENST00000379881.8 linkuse as main transcript	c.492C>T	p.Ser164=	synonymous_variant	5/11	1	NM_017826.3	P1	Q9NX45-1
SOHLH2	ENST00000317764.6 linkuse as main transcript	c.492C>T	p.Ser164=	synonymous_variant	5/7	1			Q9NX45-2

Frequencies

GnomAD3 genomes

AF:

0.0236

AC:

3583

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0630

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0105

Gnomad ASJ

AF:

0.0314

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.0187

Gnomad FIN

AF:

0.00321

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00684

Gnomad OTH

AF:

0.0205

GnomAD3 exomes

AF:

0.0133

AC:

3352

AN:

251332

Hom.:

AF XY:

0.0132

AC XY:

1796

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.0604

Gnomad AMR exome

AF:

0.00766

Gnomad ASJ exome

AF:

0.0358

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.0223

Gnomad FIN exome

AF:

0.00259

Gnomad NFE exome

AF:

0.00804

Gnomad OTH exome

AF:

0.0139

GnomAD4 exome

AF:

0.00849

AC:

12405

AN:

1461626

Hom.:

190

Cov.:

AF XY:

0.00889

AC XY:

6464

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.0629

Gnomad4 AMR exome

AF:

0.00888

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0215

Gnomad4 FIN exome

AF:

0.00288

Gnomad4 NFE exome

AF:

0.00533

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0236

AC:

3589

AN:

152218

Hom.:

Cov.:

AF XY:

0.0230

AC XY:

1711

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0630

Gnomad4 AMR

AF:

0.0105

Gnomad4 ASJ

AF:

0.0314

Gnomad4 EAS

AF:

0.000774

Gnomad4 SAS

AF:

0.0185

Gnomad4 FIN

AF:

0.00321

Gnomad4 NFE

AF:

0.00684

Gnomad4 OTH

AF:

0.0208

Alfa

AF:

0.0126

Hom.:

Bravo

AF:

0.0254

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.0108

EpiControl

AF:

0.0111

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SOHLH2-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 07, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.1

DANN

Benign

0.49

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

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