chr5-730156-A-G

Position:

• chr5-730156-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351303.2(ZDHHC11B):​c.1058+278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 148,718 control chromosomes in the GnomAD database, including 3,089 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 0.21 (3089 hom., cov: 37)
• Consequence: ZDHHC11B NM_001351303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC11B	NM_001351303.2	c.1058+278T>C		intron_variant		ENST00000508859.8	NP_001338232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC11B	ENST00000508859.8	c.1058+278T>C		intron_variant		5	NM_001351303.2	ENSP00000442373.2
ZDHHC11B	ENST00000522356.3	n.*1762+278T>C		intron_variant		2		ENSP00000505988.1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 31836 AN: 148596 Hom.: 3093 Cov.: 37

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.214 AC: 31843 AN: 148718 Hom.: 3089 Cov.: 37 AF XY: 0.215 AC XY: 15611 AN XY: 72680

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.200

Alfa AF: 0.245 Hom.: 2089

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.77

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

LitVar

Other links and lift over

dbSNP: rs436354; hg19: chr5-730271;