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GeneBe

17-58565748-A-G

Variant summary

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

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 (★).

Frequency

Genomes: 𝑓 0.16 ( 2450 hom., cov: 32)
Exomes 𝑓: 0.20 ( 31382 hom. )

Consequence

TEX14
NM_031272.5 splice_region, synonymous

Scores

2
Splicing: ADA: 0.00007911
2

Clinical Significance

Benign criteria provided, single submitter 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]

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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=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-58565748-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 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=-0.134 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
TEX14NM_031272.5 linkuse as main transcriptc.3963T>C p.Asn1321= splice_region_variant, synonymous_variant 27/32 ENST00000349033.10
TEX14NM_001201457.2 linkuse as main transcriptc.4101T>C p.Asn1367= splice_region_variant, synonymous_variant 28/33
TEX14NM_198393.4 linkuse as main transcriptc.4083T>C p.Asn1361= splice_region_variant, synonymous_variant 28/33

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEX14ENST00000349033.10 linkuse as main transcriptc.3963T>C p.Asn1321= splice_region_variant, synonymous_variant 27/325 NM_031272.5 A2Q8IWB6-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.164
AC:
24941
AN:
152056
Hom.:
2448
Cov.:
32
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.:
30
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.164
AC:
24954
AN:
152174
Hom.:
2450
Cov.:
32
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: criteria provided, single submitter
LINK: link

Submissions by phenotype

TEX14-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 17, 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
-0.84
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.

Other links and lift over

dbSNP: rs34818467; hg19: chr17-56643109; COSMIC: COSV53617818; COSMIC: COSV53617818; API