Variant rs34188981 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_024702.3(ZNF750):c.1062C>T(p.Thr354Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 1,614,108 control chromosomes in the GnomAD database, including 789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 247 hom., cov: 32)

Exomes 𝑓: 0.022 ( 542 hom. )

Consequence

ZNF750
NM_024702.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

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 links:

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:

TBCD (HGNC:):

TBCD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 17-82831393-G-A is Benign according to our data. Variant chr17-82831393-G-A is described in ClinVar as [Benign]. Clinvar id is 1290639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.02 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF750	NM_024702.3 linkuse as main transcript	c.1062C>T	p.Thr354Thr	synonymous_variant	2/3	ENST00000269394.4	NP_078978.2	Q32MQ0
TBCD	NM_005993.5 linkuse as main transcript	c.1318+16459G>A		intron_variant		ENST00000355528.9	NP_005984.3	Q9BTW9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF750	ENST00000269394.4 linkuse as main transcript	c.1062C>T	p.Thr354Thr	synonymous_variant	2/3	1	NM_024702.3	ENSP00000269394.3		Q32MQ0
TBCD	ENST00000355528.9 linkuse as main transcript	c.1318+16459G>A		intron_variant		1	NM_005993.5	ENSP00000347719.4		Q9BTW9-1

Frequencies

GnomAD3 genomes

AF:

0.0414

AC:

6298

AN:

152110

Hom.:

248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0183

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0126

Gnomad FIN

AF:

0.00377

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0212

Gnomad OTH

AF:

0.0301

GnomAD3 exomes

AF:

0.0224

AC:

5635

AN:

251456

Hom.:

151

AF XY:

0.0209

AC XY:

2839

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.113

Gnomad AMR exome

AF:

0.0105

Gnomad ASJ exome

AF:

0.00923

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0160

Gnomad FIN exome

AF:

0.00591

Gnomad NFE exome

AF:

0.0230

Gnomad OTH exome

AF:

0.0178

GnomAD4 exome

AF:

0.0217

AC:

31770

AN:

1461880

Hom.:

542

Cov.:

AF XY:

0.0211

AC XY:

15366

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.0114

Gnomad4 ASJ exome

AF:

0.00960

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0159

Gnomad4 FIN exome

AF:

0.00680

Gnomad4 NFE exome

AF:

0.0217

Gnomad4 OTH exome

AF:

0.0223

GnomAD4 genome

AF:

0.0414

AC:

6298

AN:

152228

Hom.:

247

Cov.:

AF XY:

0.0396

AC XY:

2949

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.0183

Gnomad4 ASJ

AF:

0.00922

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0126

Gnomad4 FIN

AF:

0.00377

Gnomad4 NFE

AF:

0.0211

Gnomad4 OTH

AF:

0.0298

Alfa

AF:

0.0290

Hom.:

Bravo

AF:

0.0451

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.0182

EpiControl

AF:

0.0184

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.8

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over