rs2609998

chr8-56447475-G-A

Variant summary

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

The NR_125813.1(PENK-AS1):n.694+975G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,368 control chromosomes in the GnomAD database, including 12,037 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 0.39 (12037 hom., cov: 29)
• Consequence: PENK-AS1 NR_125813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PENK-AS1	NR_125813.1	n.694+975G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PENK-AS1	ENST00000662661.1	n.264+975G>A		intron_variant, non_coding_transcript_variant
PENK-AS1	ENST00000518662.5	n.694+975G>A		intron_variant, non_coding_transcript_variant		2
PENK-AS1	ENST00000685796.1	n.657+975G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58318 AN: 151250 Hom.: 12029 Cov.: 29

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.385 AC: 58347 AN: 151368 Hom.: 12037 Cov.: 29 AF XY: 0.388 AC XY: 28659 AN XY: 73870

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.392

Alfa AF: 0.419 Hom.: 1517

Bravo AF: 0.366

Asia WGS AF: 0.413 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.6
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2609998; hg19: chr8-57360034;