rs4796356

Variant names:

• chr17-6818471-G-C
• rs4796356
• NM_053285.2:c.356+722C>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053285.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT1	NM_053285.2	MANE Select	c.356+722C>G		intron	N/A	NP_444515.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT1	ENST00000338694.7	TSL:1 MANE Select	c.356+722C>G		intron	N/A	ENSP00000341346.2
	TEKT1	ENST00000573966.1	TSL:3	n.318-2509C>G		intron	N/A
	TEKT1	ENST00000575592.1	TSL:2	n.191-2509C>G		intron	N/A	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

African (AFR) AF: 0.132 AC: 5458 AN: 41492

American (AMR) AF: 0.254 AC: 3876 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2195 AN: 5156

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4812

European-Finnish (FIN) AF: 0.267 AC: 2823 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17894 AN: 67966

Other (OTH) AF: 0.223 AC: 470 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.65
PhyloP100		0.73
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: rs4796356; hg19: chr17-6721790;