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GeneBe

17-58559493-T-C

Variant summary

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

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 (★).

Frequency

Genomes: 𝑓 0.84 ( 54115 hom., cov: 31)
Exomes 𝑓: 0.81 ( 460215 hom. )

Consequence

TEX14
NM_031272.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.11 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
TEX14NM_031272.5 linkuse as main transcriptc.4227A>G p.Glu1409= synonymous_variant 30/32 ENST00000349033.10
TEX14NM_001201457.2 linkuse as main transcriptc.4365A>G p.Glu1455= synonymous_variant 31/33
TEX14NM_198393.4 linkuse as main transcriptc.4347A>G p.Glu1449= synonymous_variant 31/33

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX14ENST00000349033.10 linkuse as main transcriptc.4227A>G p.Glu1409= synonymous_variant 30/325 NM_031272.5 A2Q8IWB6-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.841
AC:
127948
AN:
152108
Hom.:
54049
Cov.:
31
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.:
26
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.841
AC:
128075
AN:
152226
Hom.:
54115
Cov.:
31
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: criteria provided, single submitter
LINK: link

Submissions by phenotype

TEX14-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 16, 2019This 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.

Other links and lift over

dbSNP: rs7225128; hg19: chr17-56636854; COSMIC: COSV53622653; COSMIC: COSV53622653; API