chr5-737248-A-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001351303.2(ZDHHC11B):​c.936-3409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351303.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC11B	NM_001351303.2	MANE Select	c.936-3409T>C		intron	N/A	NP_001338232.1
	ZDHHC11B	NR_147095.2		n.2271-3409T>C		intron	N/A
	ZDHHC11B	NR_147096.2		n.1306-3409T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC11B	ENST00000508859.8	TSL:5 MANE Select	c.936-3409T>C		intron	N/A	ENSP00000442373.2
	ZDHHC11B	ENST00000522356.3	TSL:2	n.*937-3409T>C		intron	N/A	ENSP00000505988.1

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-0.82

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;