rs4796561

Variant names:

• chr17-6812403-G-A
• rs4796561
• NM_053285.2:c.852+428C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEKT1	NM_053285.2	c.852+428C>T		intron_variant	Intron 6 of 7	ENST00000338694.7	NP_444515.1
TEKT1	XM_011524027.4	c.852+428C>T		intron_variant	Intron 6 of 6		XP_011522329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT1	ENST00000338694.7	c.852+428C>T		intron_variant	Intron 6 of 7	1	NM_053285.2	ENSP00000341346.2
TEKT1	ENST00000572291.1	c.237+428C>T		intron_variant	Intron 2 of 2	5		ENSP00000458518.1
TEKT1	ENST00000571744.1	c.186+428C>T		intron_variant	Intron 1 of 1	3		ENSP00000460197.2
TEKT1	ENST00000575592.1	n.*443+428C>T		intron_variant	Intron 5 of 6	2		ENSP00000460359.1

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

African (AFR) AF: 0.497 AC: 20585 AN: 41424

American (AMR) AF: 0.481 AC: 7337 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3114 AN: 5160

South Asian (SAS) AF: 0.477 AC: 2293 AN: 4804

European-Finnish (FIN) AF: 0.521 AC: 5482 AN: 10524

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29103 AN: 67930

Other (OTH) AF: 0.436 AC: 912 AN: 2094

Alfa AF: 0.436 Hom.: 31776

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
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4796561; hg19: chr17-6715722;