chr9-14649730-G-A

Variant names:

• chr9-14649730-G-A
• rs10961636
• NM_178566.6:c.504+9019C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178566.6(ZDHHC21):​c.504+9019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,904 control chromosomes in the GnomAD database, including 3,319 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 0.20 (3319 hom., cov: 32)
• Consequence: ZDHHC21 NM_178566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 5 publications found

Genes affected

ZDHHC21 (HGNC:20750): (zinc finger DHHC-type palmitoyltransferase 21) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178566.6. 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
	ZDHHC21	NM_178566.6	MANE Select	c.504+9019C>T		intron	N/A	NP_848661.1
	ZDHHC21	NM_001354118.2		c.504+9019C>T		intron	N/A	NP_001341047.1
	ZDHHC21	NM_001354119.2		c.504+9019C>T		intron	N/A	NP_001341048.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC21	ENST00000380916.9	TSL:1 MANE Select	c.504+9019C>T		intron	N/A	ENSP00000370303.3
	ZDHHC21	ENST00000850567.1		c.213+9019C>T		intron	N/A	ENSP00000520857.1
	ZDHHC21	ENST00000850565.1		c.-21-30048C>T		intron	N/A	ENSP00000520856.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30959 AN: 151786 Hom.: 3315 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.204 AC: 30980 AN: 151904 Hom.: 3319 Cov.: 32 AF XY: 0.205 AC XY: 15180 AN XY: 74224

African (AFR) AF: 0.251 AC: 10385 AN: 41430

American (AMR) AF: 0.145 AC: 2217 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1550 AN: 4826

European-Finnish (FIN) AF: 0.197 AC: 2080 AN: 10546

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11900 AN: 67914

Other (OTH) AF: 0.182 AC: 384 AN: 2106

Alfa AF: 0.180 Hom.: 7450

Bravo AF: 0.200

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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: rs10961636; hg19: chr9-14649728;