Genetic Variant TEX14:c.137-1119C>T (chr17-58631673-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_031272.5(TEX14):c.137-1119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 150,590 control chromosomes in the GnomAD database, including 18,337 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 18336 hom., cov: 29)

Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

TEX14
NM_031272.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Publications

31 publications found

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 Gene-Disease associations (from GenCC):

male infertility with azoospermia or oligozoospermia due to single gene mutation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TEX14 links:

U3 (HGNC:):

U3 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_031272.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TEX14	NM_031272.5	MANE Select	c.137-1119C>T	intron	N/A	NP_112562.3
TEX14	NM_001201457.2		c.137-1119C>T	intron	N/A	NP_001188386.1	Q8IWB6-1
TEX14	NM_198393.4		c.137-1119C>T	intron	N/A	NP_938207.2	Q8IWB6-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TEX14	ENST00000349033.10	TSL:5 MANE Select	c.137-1119C>T	intron	N/A	ENSP00000268910.8	Q8IWB6-3
TEX14	ENST00000240361.12	TSL:1	c.137-1119C>T	intron	N/A	ENSP00000240361.8	Q8IWB6-1
TEX14	ENST00000389934.7	TSL:1	c.137-1119C>T	intron	N/A	ENSP00000374584.3	Q8IWB6-2

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

72887

AN:

150506

Hom.:

18320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.553

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.521

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.557

Gnomad OTH

AF:

0.507

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.484

AC:

72938

AN:

150586

Hom.:

18336

Cov.:

AF XY:

0.481

AC XY:

35329

AN XY:

73402

show subpopulations

African (AFR)

AF:

0.410

AC:

16797

AN:

40998

American (AMR)

AF:

0.439

AC:

6642

AN:

15120

Ashkenazi Jewish (ASJ)

AF:

0.521

AC:

1807

AN:

3466

East Asian (EAS)

AF:

0.180

AC:

923

AN:

5134

South Asian (SAS)

AF:

0.335

AC:

1604

AN:

4782

European-Finnish (FIN)

AF:

0.565

AC:

5692

AN:

10068

Middle Eastern (MID)

AF:

0.572

AC:

166

AN:

290

European-Non Finnish (NFE)

AF:

0.557

AC:

37758

AN:

67738

Other (OTH)

AF:

0.503

AC:

1047

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1796

3593

5389

7186

8982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.514

Hom.:

2762

Bravo

AF:

0.466

Asia WGS

AF:

0.263

AC:

916

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

6.3

(source)

DANN

Benign

0.76

PhyloP100

1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over