rs381164

Variant names:

• chr5-737248-A-C
• rs381164
• NM_001351303.2:c.936-3409T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-737248-A-C
• chr5-737248-A-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong 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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC11B	NM_001351303.2	c.936-3409T>G		intron_variant	Intron 10 of 13	ENST00000508859.8	NP_001338232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC11B	ENST00000508859.8	c.936-3409T>G		intron_variant	Intron 10 of 13	5	NM_001351303.2	ENSP00000442373.2
ZDHHC11B	ENST00000522356.3	n.*937-3409T>G		intron_variant	Intron 11 of 15	2		ENSP00000505988.1

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0428 AC: 1280 AN: 29892

American (AMR) AF: 0.00754 AC: 102 AN: 13520

Ashkenazi Jewish (ASJ) AF: 0.00210 AC: 7 AN: 3330

East Asian (EAS) AF: 0.0280 AC: 110 AN: 3928

South Asian (SAS) AF: 0.00618 AC: 26 AN: 4208

European-Finnish (FIN) AF: 0.00260 AC: 26 AN: 9998

Middle Eastern (MID) AF: 0.00379 AC: 1 AN: 264

European-Non Finnish (NFE) AF: 0.00323 AC: 205 AN: 63464

Other (OTH) AF: 0.00871 AC: 16 AN: 1836

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs381164; hg19: chr5-737363;