Variant chr5-733800-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_001351303.2(ZDHHC11B):c.975A>G(p.Pro325=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00446 in 1,604,056 control chromosomes in the GnomAD database, including 5 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 0.0040 ( 0 hom., cov: 35)

Exomes 𝑓: 0.0045 ( 5 hom. )

Consequence

ZDHHC11B
NM_001351303.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.86

Variant links:

Genes affected

ZDHHC11B (HGNC:32962): (zinc finger DHHC-type containing 11B) Predicted to enable protein-cysteine S-palmitoyltransferase activity. Predicted to be involved in several processes, including antiviral innate immune response; peptidyl-L-cysteine S-palmitoylation; and positive regulation of defense response to virus by host. Predicted to be located in endosome membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ZDHHC11B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BP7

Synonymous conserved (PhyloP=-2.86 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC11B	NM_001351303.2 linkuse as main transcript	c.975A>G	p.Pro325=	synonymous_variant	11/14	ENST00000508859.8	NP_001338232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC11B	ENST00000508859.8 linkuse as main transcript	c.975A>G	p.Pro325=	synonymous_variant	11/14	5	NM_001351303.2	ENSP00000442373	P1
ZDHHC11B	ENST00000522356.3 linkuse as main transcript	c.*976A>G		3_prime_UTR_variant, NMD_transcript_variant	12/16	2		ENSP00000505988

Frequencies

GnomAD3 genomes

AF:

0.00400

AC:

592

AN:

148126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000999

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00494

Gnomad ASJ

AF:

0.00146

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00148

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0197

Gnomad NFE

AF:

0.00669

Gnomad OTH

AF:

0.00547

GnomAD3 exomes

AF:

0.00354

AC:

881

AN:

248654

Hom.:

AF XY:

0.00367

AC XY:

494

AN XY:

134506

show subpopulations

Gnomad AFR exome

AF:

0.000956

Gnomad AMR exome

AF:

0.00363

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000985

Gnomad FIN exome

AF:

0.0000476

Gnomad NFE exome

AF:

0.00588

Gnomad OTH exome

AF:

0.00443

GnomAD4 exome

AF:

0.00451

AC:

6566

AN:

1455818

Hom.:

Cov.:

AF XY:

0.00441

AC XY:

3197

AN XY:

724420

show subpopulations

Gnomad4 AFR exome

AF:

0.000610

Gnomad4 AMR exome

AF:

0.00370

Gnomad4 ASJ exome

AF:

0.00192

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00107

Gnomad4 FIN exome

AF:

0.000170

Gnomad4 NFE exome

AF:

0.00532

Gnomad4 OTH exome

AF:

0.00452

GnomAD4 genome

AF:

0.00398

AC:

590

AN:

148238

Hom.:

Cov.:

AF XY:

0.00416

AC XY:

302

AN XY:

72524

show subpopulations

Gnomad4 AFR

AF:

0.000996

Gnomad4 AMR

AF:

0.00494

Gnomad4 ASJ

AF:

0.00146

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00148

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00668

Gnomad4 OTH

AF:

0.00541

Alfa

AF:

0.00463

Hom.:

EpiCase

AF:

0.00603

EpiControl

AF:

0.00750

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

ZDHHC11B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.59

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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