rs4143334

Variant names:

• chr6-31380423-A-G
• rs4143334
• ENST00000424108.1:n.13A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.74).
• 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 rank	MANE	Protein	UniProt
ZDHHC20P2		n.31380423A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P2	ENST00000424108.1	n.13A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298426	ENST00000755446.1	n.327-1557A>G		intron_variant	Intron 1 of 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

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) AF: 0.00 AC: 0 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.0119 AC: 496 AN: 41562

American (AMR) AF: 0.0136 AC: 208 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.134 AC: 695 AN: 5178

South Asian (SAS) AF: 0.0384 AC: 185 AN: 4818

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10616

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0243 AC: 1655 AN: 67986

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0239 Hom.: 62

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
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4143334; hg19: chr6-31348200;