rs9266689

Variant names:

• chr6-31380803-A-G
• rs9266689
• ENST00000424108.1:n.393A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 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.393A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298426	ENST00000755446.1		n.327-1177A>G		intron	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.857 AC: 12 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.492 AC: 20350 AN: 41394

American (AMR) AF: 0.652 AC: 9964 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3165 AN: 5168

South Asian (SAS) AF: 0.672 AC: 3228 AN: 4806

European-Finnish (FIN) AF: 0.701 AC: 7405 AN: 10556

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44102 AN: 67950

Other (OTH) AF: 0.602 AC: 1269 AN: 2108

Alfa AF: 0.638 Hom.: 130908

Bravo AF: 0.600

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.41
PhyloP100		0.33

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: rs9266689;

hg19: chr6-31348580;