rs4143334

chr6-31380423-A-G

Variant summary

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

The ENST00000424108.1(ZDHHC20P2):n.13A>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 0.0238 in 152,304 control chromosomes in the GnomAD database, including 74 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 0.024 (74 hom., cov: 32)
  • Exomes 𝑓: 0.017 (0 hom.)
• Consequence: ZDHHC20P2 ENST00000424108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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.13A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0236 AC: 3597 AN: 152128 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0135

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0220

GnomAD4 exome AF: 0.0172 AC: 1 AN: 58 Hom.: 0 Cov.: 0 AF XY: 0.0294 AC XY: 1 AN XY: 34

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0333

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0238 AC: 3618 AN: 152246 Hom.: 74 Cov.: 32 AF XY: 0.0247 AC XY: 1839 AN XY: 74448

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0136

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0384

Gnomad4 FIN AF: 0.0217

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0234 Hom.: 26

Bravo AF: 0.0220

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	6.7
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4143334; hg19: chr6-31348200;