chr6-31380245-G-C

Variant names:

• chr6-31380245-G-C
• rs2596571
• ENST00000755446.1:n.327-1735G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755446.1(ENSG00000298426):​n.327-1735G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,768 control chromosomes in the GnomAD database, including 43,050 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 0.75 (43050 hom., cov: 31)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 10 publications found

Genes affected

ENSG00000298426 (HGNC:):

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

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 (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-1735G>C		intron	N/A
	ZDHHC20P2	ENST00000424108.1	TSL:6	n.-166G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113651 AN: 151650 Hom.: 43007 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.749 AC: 113744 AN: 151768 Hom.: 43050 Cov.: 31 AF XY: 0.757 AC XY: 56139 AN XY: 74188

African (AFR) AF: 0.677 AC: 27986 AN: 41318

American (AMR) AF: 0.769 AC: 11735 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2974 AN: 3464

East Asian (EAS) AF: 0.924 AC: 4786 AN: 5178

South Asian (SAS) AF: 0.839 AC: 4044 AN: 4818

European-Finnish (FIN) AF: 0.831 AC: 8792 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50813 AN: 67834

Other (OTH) AF: 0.740 AC: 1562 AN: 2110

Alfa AF: 0.686 Hom.: 2308

Bravo AF: 0.736

Asia WGS AF: 0.866 AC: 3013 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	3.1
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2596571; hg19: chr6-31348022;