chr17-6801117-G-A

Variant names:

• chr17-6801117-G-A
• rs17731932
• NM_053285.2:c.853-174C>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.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
• Publications: 0 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]

TEKT1 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT1	NM_053285.2	MANE Select	c.853-174C>T		intron	N/A	NP_444515.1	Q969V4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEKT1	ENST00000338694.7	TSL:1 MANE Select	c.853-174C>T		intron	N/A	ENSP00000341346.2	Q969V4
	TEKT1	ENST00000572291.1	TSL:5	c.238-883C>T		intron	N/A	ENSP00000458518.1	I3L122
	TEKT1	ENST00000571744.1	TSL:3	c.186+11714C>T		intron	N/A	ENSP00000460197.2	I3L357

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

African (AFR) AF: 0.0895 AC: 3711 AN: 41478

American (AMR) AF: 0.148 AC: 2260 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5166

South Asian (SAS) AF: 0.117 AC: 564 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2776 AN: 10568

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9343 AN: 67984

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.0740 Hom.: 121

Bravo AF: 0.117

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.65
PhyloP100		0.16
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: rs17731932; hg19: chr17-6704436;