dbSNP rs7492357: TEDC1:c.891+236G>A (chr14-105496322-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001367178.1(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
NM_001367178.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00

Publications

2 publications found

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 Gene-Disease associations (from GenCC):

autosomal recessive primary microcephaly
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
microcephaly
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

TEDC1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEDC1	NM_001367178.1 link	c.891+236G>A		intron_variant	Intron 6 of 8	ENST00000392523.9	NP_001354107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEDC1	ENST00000392523.9 link	c.891+236G>A		intron_variant	Intron 6 of 8	1	NM_001367178.1	ENSP00000376308.4		Q86SX3-1
TEDC1	ENST00000548920.2 link	n.*111-1035G>A		intron_variant	Intron 4 of 6	5		ENSP00000450003.2		F8VP51

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

African (AFR)

AF:

0.319

AC:

3612

AN:

11316

American (AMR)

AF:

0.844

AC:

12188

AN:

14440

Ashkenazi Jewish (ASJ)

AF:

0.890

AC:

10961

AN:

12314

East Asian (EAS)

AF:

0.720

AC:

19045

AN:

26444

South Asian (SAS)

AF:

0.859

AC:

36483

AN:

42484

European-Finnish (FIN)

AF:

0.889

AC:

22129

AN:

24902

Middle Eastern (MID)

AF:

0.802

AC:

1398

AN:

1744

European-Non Finnish (NFE)

AF:

0.877

AC:

208611

AN:

237842

Other (OTH)

AF:

0.827

AC:

18796

AN:

22736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

2263

4526

6790

9053

11316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

790

1580

2370

3160

3950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.720

AC:

109521

AN:

152156

Hom.:

43994

Cov.:

AF XY:

0.725

AC XY:

53947

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.329

AC:

13648

AN:

41486

American (AMR)

AF:

0.827

AC:

12652

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.891

AC:

3093

AN:

3470

East Asian (EAS)

AF:

0.814

AC:

4201

AN:

5158

South Asian (SAS)

AF:

0.848

AC:

4097

AN:

4832

European-Finnish (FIN)

AF:

0.891

AC:

9468

AN:

10626

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.879

AC:

59718

AN:

67972

Other (OTH)

AF:

0.761

AC:

1608

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1149

2299

3448

4598

5747

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.92

PhyloP100

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over