chr1-26856493-T-G

Variant names:

• chr1-26856493-T-G
• rs10902646
• NM_032283.3:c.*2650T>G

Variant summary

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

The NM_032283.3(ZDHHC18):​c.*2650T>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 0.724 in 235,672 control chromosomes in the GnomAD database, including 63,484 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 0.71 (39654 hom., cov: 31)
  • Exomes 𝑓: 0.74 (23830 hom.)
• Consequence: ZDHHC18 NM_032283.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.53
• Publications: 5 publications found

Genes affected

ZDHHC18 (HGNC:20712): (zinc finger DHHC-type palmitoyltransferase 18) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000304862 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032283.3. 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
	ZDHHC18	NM_032283.3	MANE Select	c.*2650T>G		3_prime_UTR	Exon 8 of 8	NP_115659.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC18	ENST00000374142.9	TSL:1 MANE Select	c.*2650T>G		3_prime_UTR	Exon 8 of 8	ENSP00000363257.3
	ZDHHC18	ENST00000488397.3	TSL:2	c.*36+231T>G		intron	N/A	ENSP00000436203.1
	ENSG00000304862	ENST00000806706.1		n.94-3796A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108404 AN: 151912 Hom.: 39607 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.717

GnomAD4 exome AF: 0.744 AC: 62199 AN: 83642 Hom.: 23830 Cov.: 0 AF XY: 0.757 AC XY: 35893 AN XY: 47402

African (AFR) AF: 0.840 AC: 2881 AN: 3428

American (AMR) AF: 0.802 AC: 6139 AN: 7650

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 1182 AN: 1670

East Asian (EAS) AF: 0.998 AC: 5157 AN: 5166

South Asian (SAS) AF: 0.862 AC: 16896 AN: 19598

European-Finnish (FIN) AF: 0.647 AC: 1934 AN: 2988

Middle Eastern (MID) AF: 0.771 AC: 168 AN: 218

European-Non Finnish (NFE) AF: 0.642 AC: 25170 AN: 39230

Other (OTH) AF: 0.723 AC: 2672 AN: 3694

GnomAD4 genome AF: 0.714 AC: 108506 AN: 152030 Hom.: 39654 Cov.: 31 AF XY: 0.719 AC XY: 53443 AN XY: 74306

African (AFR) AF: 0.815 AC: 33800 AN: 41492

American (AMR) AF: 0.762 AC: 11639 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2342 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5147 AN: 5160

South Asian (SAS) AF: 0.866 AC: 4176 AN: 4820

European-Finnish (FIN) AF: 0.628 AC: 6617 AN: 10536

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42527 AN: 67956

Other (OTH) AF: 0.722 AC: 1526 AN: 2114

Alfa AF: 0.661 Hom.: 88220

Bravo AF: 0.728

Asia WGS AF: 0.927 AC: 3225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.38
PhyloP100		-5.5
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: rs10902646; hg19: chr1-27182984;