rs11924930

Positions:

• chr3-196201983-G-A
• chr3-196201983-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC19	NM_001039617.2	c.688-3109C>T		intron_variant		ENST00000296326.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC19	ENST00000296326.8	c.688-3109C>T		intron_variant		5	NM_001039617.2	P1
ZDHHC19	ENST00000397544.6	c.688-3109C>T		intron_variant, NMD_transcript_variant		1
ZDHHC19	ENST00000465519.5	n.1283-3114C>T		intron_variant, non_coding_transcript_variant		1
ZDHHC19	ENST00000438232.5	c.688-2461C>T		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.415

Alfa AF: 0.355 Hom.: 21587

Bravo AF: 0.428

Asia WGS AF: 0.232 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.44

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: rs11924930; hg19: chr3-195928854;