Variant chr17-58565748-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_031272.5(TEX14):c.3963T>C(p.Asn1321=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,603,110 control chromosomes in the GnomAD database, including 33,832 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2450 hom., cov: 32)

Exomes 𝑓: 0.20 ( 31382 hom. )

Consequence

TEX14
NM_031272.5 splice_region, synonymous

Scores

Splicing: ADA: 0.00007911

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.134

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=-0.84).

BP6

Variant 17-58565748-A-G is Benign according to our data. Variant chr17-58565748-A-G is described in ClinVar as [Benign]. Clinvar id is 3058843.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.134 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TEX14	NM_031272.5 linkuse as main transcript	c.3963T>C	p.Asn1321=	splice_region_variant, synonymous_variant	27/32	ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2 linkuse as main transcript	c.4101T>C	p.Asn1367=	splice_region_variant, synonymous_variant	28/33		NP_001188386.1
TEX14	NM_198393.4 linkuse as main transcript	c.4083T>C	p.Asn1361=	splice_region_variant, synonymous_variant	28/33		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10 linkuse as main transcript	c.3963T>C	p.Asn1321=	splice_region_variant, synonymous_variant	27/32	5	NM_031272.5	ENSP00000268910	A2	Q8IWB6-3

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24941

AN:

152056

Hom.:

2448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0633

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.0825

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.152

GnomAD3 exomes

AF:

0.174

AC:

41730

AN:

239766

Hom.:

4022

AF XY:

0.176

AC XY:

22632

AN XY:

128832

show subpopulations

Gnomad AFR exome

AF:

0.0600

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.0899

Gnomad EAS exome

AF:

0.168

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.202

AC:

293725

AN:

1450936

Hom.:

31382

Cov.:

AF XY:

0.201

AC XY:

144797

AN XY:

720686

show subpopulations

Gnomad4 AFR exome

AF:

0.0560

Gnomad4 AMR exome

AF:

0.133

Gnomad4 ASJ exome

AF:

0.0885

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.261

Gnomad4 NFE exome

AF:

0.215

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.164

AC:

24954

AN:

152174

Hom.:

2450

Cov.:

AF XY:

0.167

AC XY:

12444

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0633

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.0825

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.212

Gnomad4 OTH

AF:

0.150

Alfa

AF:

0.191

Hom.:

5118

Bravo

AF:

0.146

Asia WGS

AF:

0.163

AC:

567

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TEX14-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 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

-0.84

CADD

Benign

0.60

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000079

dbscSNV1_RF

Benign

0.0

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