rs2670028

Variant names:

• chr8-56511114-G-A
• rs2670028
• ENST00000518662.5:n.827+14759G>A

Variant summary

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

The ENST00000518662.5(PENK-AS1):​n.827+14759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,106 control chromosomes in the GnomAD database, including 43,073 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 (43073 hom., cov: 32)
• Consequence: PENK-AS1 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 2 publications found

Genes affected

PENK-AS1 (HGNC:55519): (PENK antisense RNA 1)

LINC00968 (HGNC:48727): (long intergenic non-protein coding RNA 968)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518662.5. 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
	PENK-AS1	NR_125813.1		n.827+14759G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	ENST00000518662.5	TSL:2	n.827+14759G>A		intron	N/A
	LINC00968	ENST00000519144.5	TSL:4	n.476+9007C>T		intron	N/A
	PENK-AS1	ENST00000522511.1	TSL:4	n.287-13510G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114302 AN: 151988 Hom.: 43042 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.752 AC: 114389 AN: 152106 Hom.: 43073 Cov.: 32 AF XY: 0.752 AC XY: 55885 AN XY: 74356

African (AFR) AF: 0.735 AC: 30490 AN: 41488

American (AMR) AF: 0.760 AC: 11603 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2741 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3400 AN: 5156

South Asian (SAS) AF: 0.796 AC: 3835 AN: 4818

European-Finnish (FIN) AF: 0.798 AC: 8451 AN: 10592

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.755 AC: 51317 AN: 67996

Other (OTH) AF: 0.753 AC: 1587 AN: 2108

Alfa AF: 0.749 Hom.: 70738

Bravo AF: 0.746

Asia WGS AF: 0.783 AC: 2726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2670028; hg19: chr8-57423673;