rs17731932

Positions:

• chr17-6801117-G-A
• chr17-6801117-G-C

Variant summary

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

The NM_053285.2(TEKT1):​c.853-174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,092 control chromosomes in the GnomAD database, including 1,483 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 0.13 (1483 hom., cov: 32)
• Consequence: TEKT1 NM_053285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT1	NM_053285.2	c.853-174C>T		intron_variant		ENST00000338694.7
TEKT1	XM_011524027.4	c.853-883C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT1	ENST00000338694.7	c.853-174C>T		intron_variant		1	NM_053285.2	P1
TEKT1	ENST00000571744.1	c.186+11714C>T		intron_variant		3
TEKT1	ENST00000572291.1	c.239-883C>T		intron_variant		5
TEKT1	ENST00000575592.1	c.*444-174C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19420 AN: 151974 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.128 AC: 19429 AN: 152092 Hom.: 1483 Cov.: 32 AF XY: 0.132 AC XY: 9796 AN XY: 74354

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0739 Hom.: 119

Bravo AF: 0.117

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.65

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: rs17731932; hg19: chr17-6704436;