rs1566458

Variant names:

• chr16-84985325-T-C
• rs1566458
• NM_017740.3:c.316-3331A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZDHHC7	NM_017740.3	c.316-3331A>G		intron_variant	Intron 3 of 7	ENST00000313732.9	NP_060210.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC7	ENST00000313732.9	c.316-3331A>G		intron_variant	Intron 3 of 7	1	NM_017740.3	ENSP00000315604.5
ZDHHC7	ENST00000344861.9	n.427-3331A>G		intron_variant	Intron 4 of 9	1		ENSP00000341681.5
ZDHHC7	ENST00000564466.5	c.427-3331A>G		intron_variant	Intron 4 of 8	5		ENSP00000456782.1
ZDHHC7	ENST00000569488.1	n.323+4979A>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.0990 AC: 4113 AN: 41566

American (AMR) AF: 0.286 AC: 4376 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5178

South Asian (SAS) AF: 0.186 AC: 898 AN: 4832

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10612

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13155 AN: 68010

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.190 Hom.: 8803

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
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1566458; hg19: chr16-85018931;