3-196201983-G-A

Variant names:

• chr3-196201983-G-A
• rs11924930
• NM_001039617.2:c.688-3109C>T

Variant summary

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

The NM_001039617.2(ZDHHC19):​c.688-3109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,892 control chromosomes in the GnomAD database, including 14,800 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 0.42 (14800 hom., cov: 32)
• Consequence: ZDHHC19 NM_001039617.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 13 publications found

Genes affected

ZDHHC19 (HGNC:20713): (zinc finger DHHC-type palmitoyltransferase 19) Enables protein-cysteine S-palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi membrane; endoplasmic reticulum; and perinucleolar compartment. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039617.2. 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
	ZDHHC19	NM_001039617.2	MANE Select	c.688-3109C>T		intron	N/A	NP_001034706.1
	ZDHHC19	NR_135617.2		n.773-2461C>T		intron	N/A
	ZDHHC19	NR_135618.2		n.773-3109C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC19	ENST00000296326.8	TSL:5 MANE Select	c.688-3109C>T		intron	N/A	ENSP00000296326.3
	ZDHHC19	ENST00000397544.6	TSL:1	n.688-3109C>T		intron	N/A	ENSP00000380678.2
	ZDHHC19	ENST00000465519.5	TSL:1	n.1283-3114C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63149 AN: 151774 Hom.: 14763 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.416 AC: 63244 AN: 151892 Hom.: 14800 Cov.: 32 AF XY: 0.414 AC XY: 30740 AN XY: 74240

African (AFR) AF: 0.626 AC: 25899 AN: 41380

American (AMR) AF: 0.350 AC: 5336 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.0662 AC: 341 AN: 5154

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3293 AN: 10558

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23771 AN: 67938

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.366 Hom.: 46395

Bravo AF: 0.428

Asia WGS AF: 0.232 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.44
PhyloP100		0.30
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: rs11924930; hg19: chr3-195928854;