rs17804647

chr17-6800752-G-A

Variant summary

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

The NM_053285.2(TEKT1):c.1044C>T(p.Val348=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 1,610,346 control chromosomes in the GnomAD database, including 8,200 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 0.088 (702 hom., cov: 32)
  • Exomes 𝑓: 0.097 (7498 hom.)
• Consequence: TEKT1 NM_053285.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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=-0.83).
• BP7: Synonymous conserved (PhyloP=-0.488 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT1	NM_053285.2	c.1044C>T	p.Val348=	synonymous_variant	7/8	ENST00000338694.7
TEKT1	XM_011524027.4	c.853-518C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT1	ENST00000338694.7	c.1044C>T	p.Val348=	synonymous_variant	7/8	1	NM_053285.2	P1
TEKT1	ENST00000571744.1	c.187-11422C>T		intron_variant		3
TEKT1	ENST00000572291.1	c.239-518C>T		intron_variant		5
TEKT1	ENST00000575592.1	c.*635C>T		3_prime_UTR_variant, NMD_transcript_variant	6/7	2

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13437 AN: 152000 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.104

GnomAD3 exomes AF: 0.0858 AC: 21286 AN: 248182 Hom.: 1161 AF XY: 0.0879 AC XY: 11786 AN XY: 134102

Gnomad AFR exome AF: 0.0485

Gnomad AMR exome AF: 0.0579

Gnomad ASJ exome AF: 0.138

Gnomad EAS exome AF: 0.00120

Gnomad SAS exome AF: 0.0588

Gnomad FIN exome AF: 0.105

Gnomad NFE exome AF: 0.111

Gnomad OTH exome AF: 0.120

GnomAD4 exome AF: 0.0966 AC: 140882 AN: 1458228 Hom.: 7498 Cov.: 31 AF XY: 0.0967 AC XY: 70101 AN XY: 724932

Gnomad4 AFR exome AF: 0.0546

Gnomad4 AMR exome AF: 0.0625

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.000480

Gnomad4 SAS exome AF: 0.0596

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.0884 AC: 13447 AN: 152118 Hom.: 702 Cov.: 32 AF XY: 0.0882 AC XY: 6559 AN XY: 74344

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.103

Alfa AF: 0.107 Hom.: 1573

Bravo AF: 0.0866

Asia WGS AF: 0.0340 AC: 117 AN: 3478

EpiCase AF: 0.112

EpiControl AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.1
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17804647; hg19: chr17-6704071; COSMIC: COSV58623292; COSMIC: COSV58623292;