rs8078571

chr17-6830353-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_053285.2(TEKT1):c.24A>G(p.Pro8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,591,900 control chromosomes in the GnomAD database, including 194,267 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 0.57 (26555 hom., cov: 32)
  • Exomes 𝑓: 0.48 (167712 hom.)
• Consequence: TEKT1 NM_053285.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP7: Synonymous conserved (PhyloP=-1.77 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT1	NM_053285.2	c.24A>G	p.Pro8=	synonymous_variant	2/8	ENST00000338694.7
TEKT1	XM_011524027.4	c.24A>G	p.Pro8=	synonymous_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT1	ENST00000338694.7	c.24A>G	p.Pro8=	synonymous_variant	2/8	1	NM_053285.2	P1
TEKT1	ENST00000573966.1	n.151A>G		non_coding_transcript_exon_variant	2/4	3
TEKT1	ENST00000575592.1	c.24A>G	p.Pro8=	synonymous_variant, NMD_transcript_variant	2/7	2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86214 AN: 151996 Hom.: 26505 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.522

GnomAD3 exomes AF: 0.495 AC: 113939 AN: 230082 Hom.: 29562 AF XY: 0.487 AC XY: 60805 AN XY: 124744

Gnomad AFR exome AF: 0.843

Gnomad AMR exome AF: 0.421

Gnomad ASJ exome AF: 0.441

Gnomad EAS exome AF: 0.559

Gnomad SAS exome AF: 0.494

Gnomad FIN exome AF: 0.464

Gnomad NFE exome AF: 0.466

Gnomad OTH exome AF: 0.466

GnomAD4 exome AF: 0.478 AC: 688521 AN: 1439786 Hom.: 167712 Cov.: 39 AF XY: 0.476 AC XY: 340982 AN XY: 715848

Gnomad4 AFR exome AF: 0.847

Gnomad4 AMR exome AF: 0.421

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.568

Gnomad4 SAS exome AF: 0.488

Gnomad4 FIN exome AF: 0.476

Gnomad4 NFE exome AF: 0.466

Gnomad4 OTH exome AF: 0.496

GnomAD4 genome AF: 0.567 AC: 86310 AN: 152114 Hom.: 26555 Cov.: 32 AF XY: 0.562 AC XY: 41789 AN XY: 74374

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.521

Alfa AF: 0.481 Hom.: 42354

Bravo AF: 0.578

Asia WGS AF: 0.549 AC: 1911 AN: 3478

EpiCase AF: 0.465

EpiControl AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.23
Dann	Benign	0.48

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: rs8078571; hg19: chr17-6733672; COSMIC: COSV58622658;