10-97456196-G-C

Variant names:

• chr10-97456196-G-C
• rs3818909
• NM_198046.3:c.1019+152G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZDHHC16	NM_198046.3	c.1019+152G>C		intron_variant	Intron 11 of 11	ENST00000393760.6	NP_932163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC16	ENST00000393760.6	c.1019+152G>C		intron_variant	Intron 11 of 11	1	NM_198046.3	ENSP00000377357.1

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

African (AFR) AF: 0.408 AC: 6386 AN: 15656

American (AMR) AF: 0.514 AC: 9855 AN: 19184

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 8379 AN: 14896

East Asian (EAS) AF: 0.566 AC: 18039 AN: 31888

South Asian (SAS) AF: 0.586 AC: 27828 AN: 47510

European-Finnish (FIN) AF: 0.571 AC: 20090 AN: 35202

Middle Eastern (MID) AF: 0.513 AC: 2032 AN: 3962

European-Non Finnish (NFE) AF: 0.537 AC: 231516 AN: 430806

Other (OTH) AF: 0.537 AC: 17227 AN: 32062

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

African (AFR) AF: 0.421 AC: 17463 AN: 41458

American (AMR) AF: 0.544 AC: 8320 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2006 AN: 3462

East Asian (EAS) AF: 0.599 AC: 3088 AN: 5158

South Asian (SAS) AF: 0.593 AC: 2863 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6034 AN: 10560

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37233 AN: 67948

Other (OTH) AF: 0.501 AC: 1056 AN: 2108

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
PhyloP100		-0.54
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: rs3818909; hg19: chr10-99215953;