rs9266689

Positions:

• chr6-31380803-A-G
• chr6-31380803-A-T

Variant summary

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

The ENST00000424108.1(ZDHHC20P2):​n.393A>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 0.612 in 151,954 control chromosomes in the GnomAD database, including 29,126 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 0.61 (29121 hom., cov: 31)
  • Exomes 𝑓: 0.81 (5 hom.)
• Consequence: ZDHHC20P2 ENST00000424108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P2	ENST00000424108.1	n.393A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92960 AN: 151820 Hom.: 29087 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.598

GnomAD4 exome AF: 0.813 AC: 13 AN: 16 Hom.: 5 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.857

GnomAD4 genome AF: 0.612 AC: 93040 AN: 151938 Hom.: 29121 Cov.: 31 AF XY: 0.615 AC XY: 45663 AN XY: 74252

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.602

Alfa AF: 0.646 Hom.: 53303

Bravo AF: 0.600

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9266689; hg19: chr6-31348580;