rs12098576

Variant names:

• chr10-112434994-G-A
• rs12098576
• NM_022494.3:c.736-530C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-112434994-G-A
• chr10-112434994-G-T

Variant summary

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

The NM_022494.3(ZDHHC6):​c.736-530C>T 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: 32)
• Consequence: ZDHHC6 NM_022494.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 publications found

Genes affected

ZDHHC6 (HGNC:19160): (zinc finger DHHC-type palmitoyltransferase 6) Enables palmitoyltransferase activity. Involved in positive regulation of mitochondrial fusion and protein palmitoylation. Located in 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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022494.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC6	NM_022494.3	MANE Select	c.736-530C>T		intron	N/A	NP_071939.1	Q9H6R6-1
	ZDHHC6	NM_001351082.3		c.736-530C>T		intron	N/A	NP_001338011.1	Q9H6R6-1
	ZDHHC6	NM_001351083.2		c.736-530C>T		intron	N/A	NP_001338012.1	Q9H6R6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC6	ENST00000369405.7	TSL:1 MANE Select	c.736-530C>T		intron	N/A	ENSP00000358413.3	Q9H6R6-1
	ZDHHC6	ENST00000369404.3	TSL:1	c.724-530C>T		intron	N/A	ENSP00000358412.3	Q9H6R6-2
	ZDHHC6	ENST00000682055.1		c.820-530C>T		intron	N/A	ENSP00000507388.1	A0A804HJ80

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		-0.085

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: rs12098576; hg19: chr10-114194752;