rs4143332

Variant names:

• chr6-31380588-G-A
• rs4143332
• ENST00000424108.1:n.178G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

Genes affected

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

ENSG00000298426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424108.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC20P2	ENST00000424108.1	TSL:6	n.178G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298426	ENST00000755446.1		n.327-1392G>A		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.0333 AC: 1 AN: 30

Middle Eastern (MID) AF: 0.111 AC: 2 AN: 18

European-Non Finnish (NFE) AF: 0.212 AC: 17 AN: 80

Other (OTH) AF: 0.100 AC: 1 AN: 10

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

African (AFR) AF: 0.0390 AC: 1487 AN: 38140

American (AMR) AF: 0.0412 AC: 566 AN: 13736

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 158 AN: 3278

East Asian (EAS) AF: 0.00525 AC: 24 AN: 4572

South Asian (SAS) AF: 0.0720 AC: 299 AN: 4152

European-Finnish (FIN) AF: 0.0875 AC: 824 AN: 9414

Middle Eastern (MID) AF: 0.0315 AC: 9 AN: 286

European-Non Finnish (NFE) AF: 0.121 AC: 7929 AN: 65660

Other (OTH) AF: 0.0619 AC: 119 AN: 1924

Alfa AF: 0.111 Hom.: 2529

Bravo AF: 0.0700

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.8
DANN	Benign	0.49
PhyloP100		-0.010

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4143332;

hg19: chr6-31348365;