9-14649848-C-T

Variant names:

• chr9-14649848-C-T
• rs10511594
• NM_178566.6:c.504+8901G>A

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+8901G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,746 control chromosomes in the GnomAD database, including 14,328 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 0.43 (14328 hom., cov: 32)
• Consequence: ZDHHC21 NM_178566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC21	NM_178566.6	c.504+8901G>A		intron_variant	Intron 7 of 9	ENST00000380916.9	NP_848661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.504+8901G>A		intron_variant	Intron 7 of 9	1	NM_178566.6	ENSP00000370303.3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65322 AN: 151628 Hom.: 14300 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.431 AC: 65393 AN: 151746 Hom.: 14328 Cov.: 32 AF XY: 0.432 AC XY: 32055 AN XY: 74150

African (AFR) AF: 0.496 AC: 20521 AN: 41394

American (AMR) AF: 0.391 AC: 5946 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1159 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1835 AN: 4808

European-Finnish (FIN) AF: 0.487 AC: 5129 AN: 10538

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27793 AN: 67848

Other (OTH) AF: 0.426 AC: 896 AN: 2102

Alfa AF: 0.422 Hom.: 2365

Bravo AF: 0.429

Asia WGS AF: 0.378 AC: 1315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		-0.31
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: rs10511594; hg19: chr9-14649846;