rs2719726

chr16-10685884-A-Cchr16-10685884-A-T

Variant summary

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

The NM_144674.2(TEKT5):c.719+3369T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,752 control chromosomes in the GnomAD database, including 23,521 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 0.55 (23521 hom., cov: 30)
• Consequence: TEKT5 NM_144674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

TEKT5 (HGNC:26554): (tektin 5) Predicted to be involved in cilium assembly and cilium movement involved in cell motility. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT5	NM_144674.2	c.719+3369T>G		intron_variant		ENST00000283025.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT5	ENST00000283025.7	c.719+3369T>G		intron_variant		1	NM_144674.2	P1
TEKT5	ENST00000576638.1	c.38+3369T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83247 AN: 151634 Hom.: 23488 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.549 AC: 83339 AN: 151752 Hom.: 23521 Cov.: 30 AF XY: 0.551 AC XY: 40856 AN XY: 74132

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.520

Alfa AF: 0.486 Hom.: 38410

Bravo AF: 0.559

Asia WGS AF: 0.561 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.66

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: rs2719726; hg19: chr16-10779741; COSMIC: COSV51589366;