Variant rs1386478 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001320466.2(ZDHHC23):c.*3474A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,446 control chromosomes in the GnomAD database, including 4,900 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 0.23 ( 4889 hom., cov: 32)

Exomes 𝑓: 0.26 ( 11 hom. )

Consequence

ZDHHC23
NM_001320466.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.554

Variant links:

Genes affected

ZDHHC23 (HGNC:28654): (zinc finger DHHC-type palmitoyltransferase 23) Predicted to enable protein-cysteine S-palmitoyltransferase activity. Involved in protein localization to plasma membrane and protein palmitoylation. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ZDHHC23 links:

ZDHHC23 (HGNC:):

ZDHHC23 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC23	NM_001320466.2 linkuse as main transcript	c.*3474A>G		3_prime_UTR_variant	5/5	ENST00000638807.2	NP_001307395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC23	ENST00000638807.2 linkuse as main transcript	c.*3474A>G		3_prime_UTR_variant	5/5	5	NM_001320466.2	ENSP00000492287.2		A0A1W2PRJ8

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35073

AN:

151938

Hom.:

4893

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0702

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.262

AC:

102

AN:

390

Hom.:

Cov.:

AF XY:

0.261

AC XY:

AN XY:

230

show subpopulations

Gnomad4 FIN exome

AF:

0.267

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.231

AC:

35069

AN:

152056

Hom.:

4889

Cov.:

AF XY:

0.233

AC XY:

17318

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0702

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.241

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.273

Hom.:

3326

Bravo

AF:

0.224

Asia WGS

AF:

0.279

AC:

972

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.3

DANN

Benign

0.76

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over