Genetic Variant TEX14:p.Lys1391Lys (chr17-58559547-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_031272.5(TEX14):c.4173A>G(p.Lys1391Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,514,400 control chromosomes in the GnomAD database, including 28,430 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 4231 hom., cov: 32)

Exomes 𝑓: 0.18 ( 24199 hom. )

Consequence

TEX14
NM_031272.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.581

Variant links:

Genes affected

TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

TEX14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 17-58559547-T-C is Benign according to our data. Variant chr17-58559547-T-C is described in ClinVar as [Benign]. Clinvar id is 3059694.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.581 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX14	NM_031272.5 link	c.4173A>G	p.Lys1391Lys	synonymous_variant	Exon 30 of 32	ENST00000349033.10	NP_112562.3	Q8IWB6-3
TEX14	NM_001201457.2 link	c.4311A>G	p.Lys1437Lys	synonymous_variant	Exon 31 of 33		NP_001188386.1	Q8IWB6-1
TEX14	NM_198393.4 link	c.4293A>G	p.Lys1431Lys	synonymous_variant	Exon 31 of 33		NP_938207.2	Q8IWB6-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10 link	c.4173A>G	p.Lys1391Lys	synonymous_variant	Exon 30 of 32	5	NM_031272.5	ENSP00000268910.8		Q8IWB6-3

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34313

AN:

151922

Hom.:

4224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.313

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.214

GnomAD3 exomes

AF:

0.213

AC:

53358

AN:

250412

Hom.:

6323

AF XY:

0.219

AC XY:

29586

AN XY:

135332

show subpopulations

Gnomad AFR exome

AF:

0.304

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.265

Gnomad EAS exome

AF:

0.316

Gnomad SAS exome

AF:

0.312

Gnomad FIN exome

AF:

0.197

Gnomad NFE exome

AF:

0.185

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.181

AC:

246613

AN:

1362360

Hom.:

24199

Cov.:

AF XY:

0.187

AC XY:

127813

AN XY:

682740

show subpopulations

Gnomad4 AFR exome

AF:

0.293

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.259

Gnomad4 EAS exome

AF:

0.271

Gnomad4 SAS exome

AF:

0.305

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.163

Gnomad4 OTH exome

AF:

0.207

GnomAD4 genome

AF:

0.226

AC:

34346

AN:

152040

Hom.:

4231

Cov.:

AF XY:

0.227

AC XY:

16855

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.304

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.269

Gnomad4 EAS

AF:

0.312

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.194

Gnomad4 NFE

AF:

0.185

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.197

Hom.:

3976

Bravo

AF:

0.224

Asia WGS

AF:

0.326

AC:

1132

AN:

3476

EpiCase

AF:

0.190

EpiControl

AF:

0.191

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TEX14-related disorder

Benign:1

Nov 08, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.83

CADD

Benign

4.6

DANN

Benign

0.65

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