16-85018048-T-C

Variant names:

• chr16-85018048-T-C
• rs1318275
• ENST00000728089.1:n.862A>G

Variant summary

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

The ENST00000728089.1(ENSG00000289551):​n.862A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,876 control chromosomes in the GnomAD database, including 7,086 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 0.26 (7086 hom., cov: 31)
• Consequence: ENSG00000289551 ENST00000728089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 4 publications found

Genes affected

ENSG00000289551 (HGNC:):

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC7	XM_047434352.1	c.-104+9450A>G		intron_variant	Intron 1 of 8		XP_047290308.1
ZDHHC7	XM_047434355.1	c.-104+9450A>G		intron_variant	Intron 1 of 7		XP_047290311.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289551	ENST00000728089.1	n.862A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000289551	ENST00000728087.1	n.115-3046A>G		intron_variant	Intron 1 of 1
ENSG00000289551	ENST00000728088.1	n.100-2630A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39505 AN: 151758 Hom.: 7072 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.261 AC: 39570 AN: 151876 Hom.: 7086 Cov.: 31 AF XY: 0.259 AC XY: 19216 AN XY: 74246

African (AFR) AF: 0.505 AC: 20848 AN: 41316

American (AMR) AF: 0.217 AC: 3309 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1640 AN: 5146

South Asian (SAS) AF: 0.270 AC: 1299 AN: 4804

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10020 AN: 67990

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.197 Hom.: 10549

Bravo AF: 0.280

Asia WGS AF: 0.280 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1318275; hg19: chr16-85051654;