rs381164

chr5-737248-A-Cchr5-737248-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001351303.2(ZDHHC11B):c.936-3409T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 131,316 control chromosomes in the GnomAD database, including 26 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 0.014 (26 hom., cov: 28)
• Consequence: ZDHHC11B NM_001351303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

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=-0.98).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0135 (1773/131316) while in subpopulation AFR AF= 0.0428 (1280/29892). AF 95% confidence interval is 0.0409. There are 26 homozygotes in gnomad4. There are 857 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC11B	NM_001351303.2	c.936-3409T>G		intron_variant		ENST00000508859.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC11B	ENST00000508859.8	c.936-3409T>G		intron_variant		5	NM_001351303.2	P1
ZDHHC11B	ENST00000522356.3	c.*937-3409T>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 1764 AN: 131212 Hom.: 26 Cov.: 28

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00748

Gnomad ASJ AF: 0.00210

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.00617

Gnomad FIN AF: 0.00260

Gnomad MID AF: 0.00357

Gnomad NFE AF: 0.00323

Gnomad OTH AF: 0.00881

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

GnomAD4 genome AF: 0.0135 AC: 1773 AN: 131316 Hom.: 26 Cov.: 28 AF XY: 0.0133 AC XY: 857 AN XY: 64406

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.00754

Gnomad4 ASJ AF: 0.00210

Gnomad4 EAS AF: 0.0280

Gnomad4 SAS AF: 0.00618

Gnomad4 FIN AF: 0.00260

Gnomad4 NFE AF: 0.00323

Gnomad4 OTH AF: 0.00871

Alfa AF: 0.0521 Hom.: 39

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.98
Dann	Benign	0.62

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: rs381164; hg19: chr5-737363;