rs2576581

Variant names:

• chr8-56453391-G-A
• rs2576581
• ENST00000518662.5:n.694+6891G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-56453391-G-A
• chr8-56453391-G-C
• chr8-56453391-G-T

Variant summary

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

The ENST00000518662.5(PENK-AS1):​n.694+6891G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,008 control chromosomes in the GnomAD database, including 13,764 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 0.42 (13764 hom., cov: 33)
• Consequence: PENK-AS1 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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.694+6891G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	ENST00000518662.5	TSL:2	n.694+6891G>A		intron	N/A
	PENK-AS1	ENST00000662661.1		n.264+6891G>A		intron	N/A
	PENK-AS1	ENST00000685796.1		n.657+6891G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63198 AN: 151890 Hom.: 13753 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.416 AC: 63230 AN: 152008 Hom.: 13764 Cov.: 33 AF XY: 0.419 AC XY: 31165 AN XY: 74304

African (AFR) AF: 0.289 AC: 11983 AN: 41452

American (AMR) AF: 0.384 AC: 5871 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1719 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2136 AN: 5184

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4818

European-Finnish (FIN) AF: 0.544 AC: 5733 AN: 10540

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.467 AC: 31747 AN: 67946

Other (OTH) AF: 0.414 AC: 873 AN: 2110

Alfa AF: 0.448 Hom.: 20022

Bravo AF: 0.398

Asia WGS AF: 0.477 AC: 1651 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.66
DANN	Benign	0.91
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2576581; hg19: chr8-57365950;