rs1393957

chr11-19151364-C-T

Variant summary

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

The NM_019028.3(ZDHHC13):c.584+573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,736 control chromosomes in the GnomAD database, including 21,352 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 0.48 (21352 hom., cov: 32)
• Consequence: ZDHHC13 NM_019028.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

ZDHHC13 (HGNC:18413): (zinc finger DHHC-type palmitoyltransferase 13) Predicted to enable magnesium ion transmembrane transporter activity and palmitoyltransferase activity. Involved in positive regulation of I-kappaB kinase/NF-kappaB signaling. Located in endoplasmic reticulum. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC13	NM_019028.3	c.584+573C>T		intron_variant		ENST00000446113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC13	ENST00000446113.7	c.584+573C>T		intron_variant		1	NM_019028.3	P1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72746 AN: 151618 Hom.: 21350 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.591

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.479 AC: 72751 AN: 151736 Hom.: 21352 Cov.: 32 AF XY: 0.482 AC XY: 35747 AN XY: 74150

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.492

Alfa AF: 0.582 Hom.: 15131

Bravo AF: 0.470

Asia WGS AF: 0.464 AC: 1608 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.56

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: rs1393957; hg19: chr11-19172911;