rs2251984

chr16-10694249-A-Gchr16-10694249-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.564+61T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 1,480,294 control chromosomes in the GnomAD database, including 215,319 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 0.57 (25628 hom., cov: 32)
  • Exomes 𝑓: 0.53 (189691 hom.)
• Consequence: TEKT5 NM_144674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEKT5	NM_144674.2	c.564+61T>C		intron_variant		ENST00000283025.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEKT5	ENST00000283025.7	c.564+61T>C		intron_variant		1	NM_144674.2	P1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87303 AN: 151944 Hom.: 25601 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.532 AC: 707197 AN: 1328232 Hom.: 189691 AF XY: 0.530 AC XY: 344683 AN XY: 649772

Gnomad4 AFR exome AF: 0.688

Gnomad4 AMR exome AF: 0.664

Gnomad4 ASJ exome AF: 0.424

Gnomad4 EAS exome AF: 0.610

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.559

Gnomad4 NFE exome AF: 0.526

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome AF: 0.575 AC: 87383 AN: 152062 Hom.: 25628 Cov.: 32 AF XY: 0.576 AC XY: 42792 AN XY: 74300

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.544

Alfa AF: 0.521 Hom.: 42575

Bravo AF: 0.582

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.44

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: rs2251984; hg19: chr16-10788106; COSMIC: COSV51586876; COSMIC: COSV51586876;