rs399393

chr1-36088072-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_014466.3(TEKT2):c.1179A>G(p.Thr393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 1,612,964 control chromosomes in the GnomAD database, including 686,516 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.92 (64981 hom., cov: 33)
  • Exomes 𝑓: 0.92 (621535 hom.)
• Consequence: TEKT2 NM_014466.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.78

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]

ACMG classification

Verdict is Benign. Variant got -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-36088072-A-G is Benign according to our data. Variant chr1-36088072-A-G is described in ClinVar as [Benign]. Clinvar id is 1180264.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.78 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	UniProt
TEKT2	NM_014466.3	c.1179A>G	p.Thr393=	synonymous_variant	10/10	ENST00000207457.8
TEKT2	XM_005270753.3	c.1179A>G	p.Thr393=	synonymous_variant	10/10
TEKT2	XM_011541258.4	c.1179A>G	p.Thr393=	synonymous_variant	10/10
TEKT2	XM_017001055.2	c.1179A>G	p.Thr393=	synonymous_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT2	ENST00000207457.8	c.1179A>G	p.Thr393=	synonymous_variant	10/10	1	NM_014466.3	P1
TEKT2	ENST00000473120.1	c.*261A>G		3_prime_UTR_variant	3/3	3
TEKT2	ENST00000469024.1	c.*983A>G		3_prime_UTR_variant, NMD_transcript_variant	10/10	2

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140466 AN: 152152 Hom.: 64924 Cov.: 33

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.919

GnomAD3 exomes AF: 0.927 AC: 231707 AN: 249926 Hom.: 107523 AF XY: 0.925 AC XY: 125243 AN XY: 135442

Gnomad AFR exome AF: 0.916

Gnomad AMR exome AF: 0.962

Gnomad ASJ exome AF: 0.904

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.916

Gnomad FIN exome AF: 0.904

Gnomad NFE exome AF: 0.916

Gnomad OTH exome AF: 0.926

GnomAD4 exome AF: 0.922 AC: 1347205 AN: 1460694 Hom.: 621535 Cov.: 74 AF XY: 0.922 AC XY: 669620 AN XY: 726618

Gnomad4 AFR exome AF: 0.918

Gnomad4 AMR exome AF: 0.960

Gnomad4 ASJ exome AF: 0.901

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.913

Gnomad4 FIN exome AF: 0.904

Gnomad4 NFE exome AF: 0.920

Gnomad4 OTH exome AF: 0.923

GnomAD4 genome AF: 0.923 AC: 140581 AN: 152270 Hom.: 64981 Cov.: 33 AF XY: 0.923 AC XY: 68743 AN XY: 74444

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.921

Alfa AF: 0.919 Hom.: 81819

Bravo AF: 0.925

Asia WGS AF: 0.969 AC: 3369 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.61
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs399393; hg19: chr1-36553673;