rs3818909

Positions:

• chr10-97456196-G-C
• chr10-97456196-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198046.3(ZDHHC16):​c.1019+152G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 783,168 control chromosomes in the GnomAD database, including 114,258 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 0.52 (20715 hom., cov: 32)
  • Exomes 𝑓: 0.54 (93543 hom.)
• Consequence: ZDHHC16 NM_198046.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

ZDHHC16 (HGNC:20714): (zinc finger DHHC-type palmitoyltransferase 16) Enables palmitoyltransferase activity. Involved in protein palmitoylation. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC16	NM_198046.3	c.1019+152G>C		intron_variant		ENST00000393760.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC16	ENST00000393760.6	c.1019+152G>C		intron_variant		1	NM_198046.3	P4

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78714 AN: 151884 Hom.: 20694 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.541 AC: 341352 AN: 631166 Hom.: 93543 Cov.: 8 AF XY: 0.543 AC XY: 176125 AN XY: 324198

Gnomad4 AFR exome AF: 0.408

Gnomad4 AMR exome AF: 0.514

Gnomad4 ASJ exome AF: 0.563

Gnomad4 EAS exome AF: 0.566

Gnomad4 SAS exome AF: 0.586

Gnomad4 FIN exome AF: 0.571

Gnomad4 NFE exome AF: 0.537

Gnomad4 OTH exome AF: 0.537

GnomAD4 genome AF: 0.518 AC: 78775 AN: 152002 Hom.: 20715 Cov.: 32 AF XY: 0.522 AC XY: 38804 AN XY: 74310

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.501

Alfa AF: 0.397 Hom.: 1112

Bravo AF: 0.505

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs3818909; hg19: chr10-99215953;