rs4796356

Positions:

• chr17-6818471-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_053285.2(TEKT1):​c.356+722C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,048 control chromosomes in the GnomAD database, including 4,410 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4410 hom., cov: 32)
• Consequence: TEKT1 NM_053285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730

Genes affected

TEKT1 (HGNC:15534): (tektin 1) 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 predominantly expressed in the testis and in mouse, tektin 1 mRNA was localized to the spermatocytes and round spermatids in the seminiferous tubules, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

TEKT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEKT1	NM_053285.2	c.356+722C>G		intron_variant		ENST00000338694.7	NP_444515.1
TEKT1	XM_011524027.4	c.356+722C>G		intron_variant			XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEKT1	ENST00000338694.7	c.356+722C>G		intron_variant		1	NM_053285.2	ENSP00000341346.2
TEKT1	ENST00000573966.1	n.318-2509C>G		intron_variant		3
TEKT1	ENST00000575592.1	n.191-2509C>G		intron_variant		2		ENSP00000460359.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34943 AN: 151930 Hom.: 4413 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.222

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.230 AC: 34945 AN: 152048 Hom.: 4410 Cov.: 32 AF XY: 0.231 AC XY: 17174 AN XY: 74334

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.223

Alfa AF: 0.240 Hom.: 647

Bravo AF: 0.226

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.65

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: rs4796356; hg19: chr17-6721790;