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GeneBe

1-36087239-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_014466.3(TEKT2):c.783G>A(p.Thr261=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,614,114 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 9 hom. )

Consequence

TEKT2
NM_014466.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.82
Variant links:
Genes affected
TEKT2 (HGNC:11725): (tektin 2) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. This gene is expressed in the testis and its protein is localized to the flagella of the sperms, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 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=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-36087239-G-A is Benign according to our data. Variant chr1-36087239-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638662.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=-2.82 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEKT2NM_014466.3 linkuse as main transcriptc.783G>A p.Thr261= synonymous_variant 7/10 ENST00000207457.8
TEKT2XM_005270753.3 linkuse as main transcriptc.783G>A p.Thr261= synonymous_variant 7/10
TEKT2XM_011541258.4 linkuse as main transcriptc.783G>A p.Thr261= synonymous_variant 7/10
TEKT2XM_017001055.2 linkuse as main transcriptc.783G>A p.Thr261= synonymous_variant 7/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEKT2ENST00000207457.8 linkuse as main transcriptc.783G>A p.Thr261= synonymous_variant 7/101 NM_014466.3 P1
TEKT2ENST00000469024.1 linkuse as main transcriptc.*587G>A 3_prime_UTR_variant, NMD_transcript_variant 7/102
TEKT2ENST00000473120.1 linkuse as main transcript upstream_gene_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00127
AC:
194
AN:
152188
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00547
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00198
Gnomad OTH
AF:
0.00334
GnomAD3 exomes
AF:
0.00135
AC:
339
AN:
251406
Hom.:
1
AF XY:
0.00127
AC XY:
173
AN XY:
135898
show subpopulations
Gnomad AFR exome
AF:
0.000369
Gnomad AMR exome
AF:
0.000983
Gnomad ASJ exome
AF:
0.00387
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.00215
Gnomad OTH exome
AF:
0.00196
GnomAD4 exome
AF:
0.00213
AC:
3109
AN:
1461808
Hom.:
9
Cov.:
33
AF XY:
0.00201
AC XY:
1464
AN XY:
727206
show subpopulations
Gnomad4 AFR exome
AF:
0.000388
Gnomad4 AMR exome
AF:
0.00105
Gnomad4 ASJ exome
AF:
0.00471
Gnomad4 EAS exome
AF:
0.000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.000206
Gnomad4 NFE exome
AF:
0.00250
Gnomad4 OTH exome
AF:
0.00197
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00127
AC:
194
AN:
152306
Hom.:
0
Cov.:
32
AF XY:
0.00105
AC XY:
78
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00547
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00198
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00171
Hom.:
0
Bravo
AF:
0.00132
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00273
EpiControl
AF:
0.00207

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023TEKT2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
2.5
Dann
Benign
0.80

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs146736752; hg19: chr1-36552840; COSMIC: COSV52881307; COSMIC: COSV52881307; API