6-157493974-G-C

Variant names:

• chr6-157493974-G-C
• rs4709298
• NM_024630.3:c.246-48611G>C

Variant summary

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

The NM_024630.3(ZDHHC14):​c.246-48611G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,058 control chromosomes in the GnomAD database, including 11,539 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 0.38 (11539 hom., cov: 33)
• Consequence: ZDHHC14 NM_024630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 1 publications found

Genes affected

ZDHHC14 (HGNC:20341): (zinc finger DHHC-type palmitoyltransferase 14) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in endoplasmic reticulum. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024630.3. 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
	ZDHHC14	NM_024630.3	MANE Select	c.246-48611G>C		intron	N/A	NP_078906.2
	ZDHHC14	NM_153746.2		c.246-48611G>C		intron	N/A	NP_714968.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC14	ENST00000359775.10	TSL:1 MANE Select	c.246-48611G>C		intron	N/A	ENSP00000352821.5
	ZDHHC14	ENST00000414563.6	TSL:1	c.246-48611G>C		intron	N/A	ENSP00000410713.2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57457 AN: 151940 Hom.: 11520 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.378 AC: 57514 AN: 152058 Hom.: 11539 Cov.: 33 AF XY: 0.382 AC XY: 28369 AN XY: 74330

African (AFR) AF: 0.256 AC: 10641 AN: 41490

American (AMR) AF: 0.502 AC: 7668 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2252 AN: 5146

South Asian (SAS) AF: 0.298 AC: 1437 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5371 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28044 AN: 67972

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.401 Hom.: 1600

Bravo AF: 0.376

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.65
PhyloP100		1.3
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: rs4709298; hg19: chr6-157915006;