1-36084643-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014466.3(TEKT2):c.-52-227G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 558,020 control chromosomes in the GnomAD database, including 2,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (739 hom., cov: 32)
  • Exomes 𝑓: 0.046 (2173 hom.)
• Consequence: TEKT2 NM_014466.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.732

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 1-36084643-G-C is Benign according to our data. Variant chr1-36084643-G-C is described in ClinVar as [Benign]. Clinvar id is 1234632.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT2	NM_014466.3	c.-52-227G>C		intron_variant		ENST00000207457.8
TEKT2	XM_005270753.3	c.-53+113G>C		intron_variant
TEKT2	XM_011541258.4	c.-52-227G>C		intron_variant
TEKT2	XM_017001055.2	c.-52-227G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT2	ENST00000207457.8	c.-52-227G>C		intron_variant		1	NM_014466.3	P1
TEKT2	ENST00000469024.1	c.-53+133G>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9337 AN: 151884 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.0681

GnomAD4 exome AF: 0.0459 AC: 18649 AN: 406018 Hom.: 2173 AF XY: 0.0436 AC XY: 9309 AN XY: 213434

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.215

Gnomad4 ASJ exome AF: 0.0167

Gnomad4 EAS exome AF: 0.335

Gnomad4 SAS exome AF: 0.0392

Gnomad4 FIN exome AF: 0.0314

Gnomad4 NFE exome AF: 0.00415

Gnomad4 OTH exome AF: 0.0426

GnomAD4 genome AF: 0.0616 AC: 9364 AN: 152002 Hom.: 739 Cov.: 32 AF XY: 0.0660 AC XY: 4904 AN XY: 74314

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.0474

Gnomad4 FIN AF: 0.0353

Gnomad4 NFE AF: 0.00379

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0345 Hom.: 51

Bravo AF: 0.0785

Asia WGS AF: 0.128 AC: 447 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	8.7
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

Other links and lift over

dbSNP: rs80034350; hg19: chr1-36550244;