rs80034350

Variant names:

• chr1-36084643-G-C
• rs80034350
• NM_014466.3:c.-52-227G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014466.3(TEKT2):​c.-52-227G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 558,020 control chromosomes in the GnomAD database, including 2,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (739 hom., cov: 32)
  • Exomes 𝑓: 0.046 (2173 hom.)
• Consequence: TEKT2 NM_014466.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.732
• Publications: 1 publications found

Genes affected

TEKT2 (HGNC:11725): (tektin 2) 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 expressed in the testis and its protein is localized to the flagella of the sperms, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 1-36084643-G-C is Benign according to our data. Variant chr1-36084643-G-C is described in ClinVar as [Benign]. Clinvar id is 1234632.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEKT2	NM_014466.3	c.-52-227G>C		intron_variant	Intron 1 of 9	ENST00000207457.8	NP_055281.2
TEKT2	XM_005270753.3	c.-53+113G>C		intron_variant	Intron 1 of 9		XP_005270810.1
TEKT2	XM_011541258.4	c.-52-227G>C		intron_variant	Intron 1 of 9		XP_011539560.1
TEKT2	XM_017001055.2	c.-52-227G>C		intron_variant	Intron 1 of 9		XP_016856544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEKT2	ENST00000207457.8	c.-52-227G>C		intron_variant	Intron 1 of 9	1	NM_014466.3	ENSP00000207457.3
TEKT2	ENST00000469024.1	n.-53+133G>C		intron_variant	Intron 1 of 9	2		ENSP00000434183.1

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9337 AN: 151884 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.0681

GnomAD4 exome AF: 0.0459 AC: 18649 AN: 406018 Hom.: 2173 AF XY: 0.0436 AC XY: 9309 AN XY: 213434

African (AFR) AF: 0.102 AC: 1187 AN: 11656

American (AMR) AF: 0.215 AC: 3713 AN: 17290

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 211 AN: 12638

East Asian (EAS) AF: 0.335 AC: 9002 AN: 26860

South Asian (SAS) AF: 0.0392 AC: 1716 AN: 43774

European-Finnish (FIN) AF: 0.0314 AC: 792 AN: 25260

Middle Eastern (MID) AF: 0.0100 AC: 18 AN: 1800

European-Non Finnish (NFE) AF: 0.00415 AC: 1010 AN: 243250

Other (OTH) AF: 0.0426 AC: 1000 AN: 23490

GnomAD4 genome AF: 0.0616 AC: 9364 AN: 152002 Hom.: 739 Cov.: 32 AF XY: 0.0660 AC XY: 4904 AN XY: 74314

African (AFR) AF: 0.100 AC: 4156 AN: 41430

American (AMR) AF: 0.179 AC: 2730 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1421 AN: 5142

South Asian (SAS) AF: 0.0474 AC: 228 AN: 4806

European-Finnish (FIN) AF: 0.0353 AC: 373 AN: 10580

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00379 AC: 258 AN: 67988

Other (OTH) AF: 0.0674 AC: 142 AN: 2106

Alfa AF: 0.0345 Hom.: 51

Bravo AF: 0.0785

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.7
DANN	Benign	0.80
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: rs80034350; hg19: chr1-36550244;