rs4143332

chr6-31380588-G-A

Variant summary

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

The ENST00000424108.1(ZDHHC20P2):n.178G>A 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 0.0814 in 142,182 control chromosomes in the GnomAD database, including 592 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 0.081 (589 hom., cov: 33)
  • Exomes 𝑓: 0.15 (3 hom.)
• Consequence: ZDHHC20P2 ENST00000424108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

ZDHHC20P2 (HGNC:33457): (zinc finger DHHC-type containing 20 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC20P2	ENST00000424108.1	n.178G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 11545 AN: 141914 Hom.: 589 Cov.: 33

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.00545

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.0327

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0626

GnomAD4 exome AF: 0.147 AC: 22 AN: 150 Hom.: 3 Cov.: 0 AF XY: 0.122 AC XY: 9 AN XY: 74

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0333

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.0813 AC: 11549 AN: 142032 Hom.: 589 Cov.: 33 AF XY: 0.0774 AC XY: 5321 AN XY: 68736

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.00525

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.110 Hom.: 423

Bravo AF: 0.0700

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4143332; hg19: chr6-31348365;