Variant 14-105496322-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000392523.9(TEDC1):c.891+236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 546,378 control chromosomes in the GnomAD database, including 187,144 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 0.72 ( 43994 hom., cov: 35)

Exomes 𝑓: 0.85 ( 143150 hom. )

Consequence

TEDC1
ENST00000392523.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00

Variant links:

Genes affected

TEDC1 (HGNC:20127): (tubulin epsilon and delta complex 1) Predicted to be involved in positive regulation of smoothened signaling pathway. Predicted to be located in centriole and cilium. [provided by Alliance of Genome Resources, Apr 2022]

TEDC1 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEDC1	NM_001367178.1 linkuse as main transcript	c.891+236G>A		intron_variant		ENST00000392523.9	NP_001354107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEDC1	ENST00000392523.9 linkuse as main transcript	c.891+236G>A		intron_variant		1	NM_001367178.1	ENSP00000376308		Q86SX3-1

Frequencies

GnomAD3 genomes

AF:

0.720

AC:

109503

AN:

152038

Hom.:

43987

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.899

Gnomad AMR

AF:

0.827

Gnomad ASJ

AF:

0.891

Gnomad EAS

AF:

0.815

Gnomad SAS

AF:

0.847

Gnomad FIN

AF:

0.891

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.879

Gnomad OTH

AF:

0.760

GnomAD4 exome

AF:

0.845

AC:

333223

AN:

394222

Hom.:

143150

Cov.:

AF XY:

0.849

AC XY:

175651

AN XY:

206910

show subpopulations

Gnomad4 AFR exome

AF:

0.319

Gnomad4 AMR exome

AF:

0.844

Gnomad4 ASJ exome

AF:

0.890

Gnomad4 EAS exome

AF:

0.720

Gnomad4 SAS exome

AF:

0.859

Gnomad4 FIN exome

AF:

0.889

Gnomad4 NFE exome

AF:

0.877

Gnomad4 OTH exome

AF:

0.827

GnomAD4 genome

AF:

0.720

AC:

109521

AN:

152156

Hom.:

43994

Cov.:

AF XY:

0.725

AC XY:

53947

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.827

Gnomad4 ASJ

AF:

0.891

Gnomad4 EAS

AF:

0.814

Gnomad4 SAS

AF:

0.848

Gnomad4 FIN

AF:

0.891

Gnomad4 NFE

AF:

0.879

Gnomad4 OTH

AF:

0.761

Alfa

AF:

0.790

Hom.:

6312

Bravo

AF:

0.697

Asia WGS

AF:

0.800

AC:

2783

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.5

DANN

Benign

0.92

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