dbSNP rs35156590: TBCD:c.1318+14486dupA (chr17-82829419-T-TA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005993.5(TBCD):c.1318+14486dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10205 hom., cov: 0)

Exomes 𝑓: 0.37 ( 153 hom. )

Consequence

TBCD
NM_005993.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327

Publications

3 publications found

Variant links:

Genes affected

TBCD (HGNC:11581): (tubulin folding cofactor D) Cofactor D is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. [provided by RefSeq, Jul 2008]

TBCD links:

ZNF750 (HGNC:25843): (zinc finger protein 750) This gene encodes a protein with a nuclear localization site and a C2H2 zinc finger domain. Mutations in this gene have been associated with seborrhea-like dermatitis with psoriasiform elements. [provided by RefSeq, Jul 2008]

ZNF750 Gene-Disease associations (from GenCC):

seborrhea-like dermatitis with psoriasiform elements
Inheritance: AD, Unknown Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)

ZNF750 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBCD	NM_005993.5 link	c.1318+14486dupA		intron_variant	Intron 13 of 38	ENST00000355528.9	NP_005984.3
ZNF750	NM_024702.3 link	c.*722dupT		downstream_gene_variant		ENST00000269394.4	NP_078978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBCD	ENST00000355528.9 link	c.1318+14485_1318+14486insA		intron_variant	Intron 13 of 38	1	NM_005993.5	ENSP00000347719.4
ZNF750	ENST00000269394.4 link	c.722_723insT		downstream_gene_variant		1	NM_024702.3	ENSP00000269394.3

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54838

AN:

152104

Hom.:

10205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.353

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.394

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.372

GnomAD4 exome

AF:

0.368

AC:

836

AN:

2272

Hom.:

153

Cov.:

AF XY:

0.369

AC XY:

424

AN XY:

1150

show subpopulations

African (AFR)

AF:

0.264

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.349

AC:

AN:

European-Finnish (FIN)

AF:

0.433

AC:

AN:

Middle Eastern (MID)

AF:

0.378

AC:

535

AN:

1414

European-Non Finnish (NFE)

AF:

0.392

AC:

175

AN:

446

Other (OTH)

AF:

0.280

AC:

AN:

168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.360

AC:

54849

AN:

152224

Hom.:

10205

Cov.:

AF XY:

0.359

AC XY:

26753

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.270

AC:

11212

AN:

41542

American (AMR)

AF:

0.403

AC:

6168

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1320

AN:

3470

East Asian (EAS)

AF:

0.380

AC:

1970

AN:

5182

South Asian (SAS)

AF:

0.346

AC:

1670

AN:

4828

European-Finnish (FIN)

AF:

0.394

AC:

4176

AN:

10590

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.399

AC:

27108

AN:

68000

Other (OTH)

AF:

0.368

AC:

777

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1870

3739

5609

7478

9348

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

544

1088

1632

2176

2720

<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:

0.153

Hom.:

281

Bravo

AF:

0.359

Asia WGS

AF:

0.360

AC:

1253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.33

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