rs1566458

Positions:

• chr16-84985325-T-C

Variant summary

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

The NM_017740.3(ZDHHC7):​c.316-3331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,280 control chromosomes in the GnomAD database, including 2,637 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 0.17 (2637 hom., cov: 32)
• Consequence: ZDHHC7 NM_017740.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

ZDHHC7 (HGNC:18459): (zinc finger DHHC-type palmitoyltransferase 7) Enables protein-cysteine S-palmitoyltransferase activity. Involved in several processes, including peptidyl-L-cysteine S-palmitoylation; polarized epithelial cell differentiation; and regulation of signal transduction. Located in Golgi apparatus and nucleoplasm. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC7	NM_017740.3	c.316-3331A>G		intron_variant		ENST00000313732.9	NP_060210.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC7	ENST00000313732.9	c.316-3331A>G		intron_variant		1	NM_017740.3	ENSP00000315604	P1
ZDHHC7	ENST00000344861.9	c.427-3331A>G		intron_variant, NMD_transcript_variant		1		ENSP00000341681
ZDHHC7	ENST00000564466.5	c.427-3331A>G		intron_variant		5		ENSP00000456782
ZDHHC7	ENST00000569488.1	n.323+4979A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26474 AN: 152162 Hom.: 2631 Cov.: 32

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.174 AC: 26510 AN: 152280 Hom.: 2637 Cov.: 32 AF XY: 0.176 AC XY: 13087 AN XY: 74468

Gnomad4 AFR AF: 0.0990

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.189

Alfa AF: 0.194 Hom.: 5773

Bravo AF: 0.182

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.27
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1566458; hg19: chr16-85018931;