Variant chr17-58559493-T-C 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.4227A>G(p.Glu1409=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 1,554,508 control chromosomes in the GnomAD database, including 514,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.84 ( 54115 hom., cov: 31)

Exomes 𝑓: 0.81 ( 460215 hom. )

Consequence

TEX14
NM_031272.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.11

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=-0.72).

BP6

Variant 17-58559493-T-C is Benign according to our data. Variant chr17-58559493-T-C is described in ClinVar as [Benign]. Clinvar id is 3060778.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.11 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.4227A>G	p.Glu1409=	synonymous_variant	30/32	ENST00000349033.10	NP_112562.3
TEX14	NM_001201457.2 linkuse as main transcript	c.4365A>G	p.Glu1455=	synonymous_variant	31/33		NP_001188386.1
TEX14	NM_198393.4 linkuse as main transcript	c.4347A>G	p.Glu1449=	synonymous_variant	31/33		NP_938207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX14	ENST00000349033.10 linkuse as main transcript	c.4227A>G	p.Glu1409=	synonymous_variant	30/32	5	NM_031272.5	ENSP00000268910	A2	Q8IWB6-3

Frequencies

GnomAD3 genomes

AF:

0.841

AC:

127948

AN:

152108

Hom.:

54049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.910

Gnomad AMI

AF:

0.821

Gnomad AMR

AF:

0.847

Gnomad ASJ

AF:

0.779

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.899

Gnomad FIN

AF:

0.831

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.809

GnomAD3 exomes

AF:

0.844

AC:

211346

AN:

250514

Hom.:

89722

AF XY:

0.839

AC XY:

113646

AN XY:

135406

show subpopulations

Gnomad AFR exome

AF:

0.915

Gnomad AMR exome

AF:

0.892

Gnomad ASJ exome

AF:

0.789

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.894

Gnomad FIN exome

AF:

0.828

Gnomad NFE exome

AF:

0.790

Gnomad OTH exome

AF:

0.810

GnomAD4 exome

AF:

0.808

AC:

1133241

AN:

1402282

Hom.:

460215

Cov.:

AF XY:

0.810

AC XY:

567783

AN XY:

700966

show subpopulations

Gnomad4 AFR exome

AF:

0.916

Gnomad4 AMR exome

AF:

0.884

Gnomad4 ASJ exome

AF:

0.787

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.892

Gnomad4 FIN exome

AF:

0.823

Gnomad4 NFE exome

AF:

0.787

Gnomad4 OTH exome

AF:

0.815

GnomAD4 genome

AF:

0.841

AC:

128075

AN:

152226

Hom.:

54115

Cov.:

AF XY:

0.845

AC XY:

62881

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.910

Gnomad4 AMR

AF:

0.847

Gnomad4 ASJ

AF:

0.779

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.900

Gnomad4 FIN

AF:

0.831

Gnomad4 NFE

AF:

0.788

Gnomad4 OTH

AF:

0.811

Alfa

AF:

0.795

Hom.:

60401

Bravo

AF:

0.845

Asia WGS

AF:

0.955

AC:

3321

AN:

3476

EpiCase

AF:

0.781

EpiControl

AF:

0.773

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 16, 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

-0.72

CADD

Benign

6.2

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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