rs4796561

chr17-6812403-G-A

Variant summary

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

The NM_053285.2(TEKT1):c.852+428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,854 control chromosomes in the GnomAD database, including 16,583 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 0.46 (16583 hom., cov: 31)
• Consequence: TEKT1 NM_053285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT1	NM_053285.2	c.852+428C>T		intron_variant		ENST00000338694.7
TEKT1	XM_011524027.4	c.852+428C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT1	ENST00000338694.7	c.852+428C>T		intron_variant		1	NM_053285.2	P1
TEKT1	ENST00000571744.1	c.186+428C>T		intron_variant		3
TEKT1	ENST00000572291.1	c.238+428C>T		intron_variant		5
TEKT1	ENST00000575592.1	c.*443+428C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70504 AN: 151736 Hom.: 16570 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.465 AC: 70544 AN: 151854 Hom.: 16583 Cov.: 31 AF XY: 0.468 AC XY: 34745 AN XY: 74206

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.436

Alfa AF: 0.433 Hom.: 19801

Bravo AF: 0.463

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.69

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: rs4796561; hg19: chr17-6715722;