Variant rs2251984 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

Variant links:

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]

TEKT5 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
TEKT5	NM_144674.2 linkuse as main transcript	c.564+61T>C		intron_variant		ENST00000283025.7	NP_653275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEKT5	ENST00000283025.7 linkuse as main transcript	c.564+61T>C		intron_variant		1	NM_144674.2	ENSP00000283025	P1

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

87303

AN:

151944

Hom.:

25601

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.576

AC XY:

42792

AN XY:

74300

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over