rs1143025

Variant names:

• chr9-14612190-T-G
• rs1143025
• NM_178566.6:c.*6776A>C

Variant summary

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

The NM_178566.6(ZDHHC21):​c.*6776A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,870 control chromosomes in the GnomAD database, including 10,517 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 0.37 (10517 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZDHHC21 NM_178566.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 4 publications found

Genes affected

ZDHHC21 (HGNC:20750): (zinc finger DHHC-type palmitoyltransferase 21) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi apparatus and plasma membrane. [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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC21	NM_178566.6	c.*6776A>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000380916.9	NP_848661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.*6776A>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_178566.6	ENSP00000370303.3

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55831 AN: 151752 Hom.: 10509 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.363

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.368 AC: 55879 AN: 151870 Hom.: 10517 Cov.: 32 AF XY: 0.369 AC XY: 27363 AN XY: 74242

African (AFR) AF: 0.308 AC: 12790 AN: 41484

American (AMR) AF: 0.303 AC: 4615 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1500 AN: 3460

East Asian (EAS) AF: 0.282 AC: 1457 AN: 5170

South Asian (SAS) AF: 0.350 AC: 1688 AN: 4828

European-Finnish (FIN) AF: 0.446 AC: 4708 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27576 AN: 67836

Other (OTH) AF: 0.370 AC: 781 AN: 2108

Alfa AF: 0.381 Hom.: 1896

Bravo AF: 0.356

Asia WGS AF: 0.369 AC: 1284 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.3
DANN	Benign	0.78
PhyloP100		0.094
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: rs1143025; hg19: chr9-14612188;