Variant chr5-751185-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001351303.2(ZDHHC11B):c.576C>T(p.Leu192Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00238 in 1,310,064 control chromosomes in the GnomAD database, including 632 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00065 ( 1 hom., cov: 10)

Exomes 𝑓: 0.0025 ( 631 hom. )

Consequence

ZDHHC11B
NM_001351303.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.641

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-751185-G-A is Benign according to our data. Variant chr5-751185-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2655255.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.641 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 631 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC11B	NM_001351303.2 link	c.576C>T	p.Leu192Leu	synonymous_variant	7/14	ENST00000508859.8	NP_001338232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZDHHC11B	ENST00000508859.8 link	c.576C>T	p.Leu192Leu	synonymous_variant	7/14	5	NM_001351303.2	ENSP00000442373.2	P0C7U3
ZDHHC11B	ENST00000522356.3 link	n.576C>T		non_coding_transcript_exon_variant	7/16	2		ENSP00000505988.1	A0A7P0TA36
ZDHHC11B	ENST00000622126.2 link	n.50C>T		non_coding_transcript_exon_variant	1/2	5
ZDHHC11B	ENST00000651714.1 link	n.*139C>T		downstream_gene_variant				ENSP00000498273.1	A0A494BZX9

Frequencies

GnomAD3 genomes

AF:

0.000634

AC:

AN:

82060

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000117

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000604

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000546

Gnomad FIN

AF:

0.00156

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000987

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00185

AC:

390

AN:

210400

Hom.:

AF XY:

0.00214

AC XY:

244

AN XY:

114208

show subpopulations

Gnomad AFR exome

AF:

0.000777

Gnomad AMR exome

AF:

0.00146

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00233

Gnomad FIN exome

AF:

0.00296

Gnomad NFE exome

AF:

0.00228

Gnomad OTH exome

AF:

0.00155

GnomAD4 exome

AF:

0.00250

AC:

3067

AN:

1227958

Hom.:

631

Cov.:

AF XY:

0.00250

AC XY:

1528

AN XY:

610582

show subpopulations

Gnomad4 AFR exome

AF:

0.000422

Gnomad4 AMR exome

AF:

0.00104

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00245

Gnomad4 FIN exome

AF:

0.00262

Gnomad4 NFE exome

AF:

0.00276

Gnomad4 OTH exome

AF:

0.00251

GnomAD4 genome

AF:

0.000646

AC:

AN:

82106

Hom.:

Cov.:

AF XY:

0.000536

AC XY:

AN XY:

39154

show subpopulations

Gnomad4 AFR

AF:

0.000155

Gnomad4 AMR

AF:

0.000604

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000546

Gnomad4 FIN

AF:

0.00156

Gnomad4 NFE

AF:

0.000987

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00145

Hom.:

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, 2022

ZDHHC11B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.2

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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