rs2670029

Positions:

• chr8-56472437-C-A
• chr8-56472437-C-G

Variant summary

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

The NR_125813.1(PENK-AS1):​n.695-23786C>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 0.446 in 151,862 control chromosomes in the GnomAD database, including 15,313 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 0.45 (15313 hom., cov: 31)
• Consequence: PENK-AS1 NR_125813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PENK-AS1	NR_125813.1	n.695-23786C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PENK-AS1	ENST00000662661.1	n.265-23786C>A		intron_variant, non_coding_transcript_variant
PENK-AS1	ENST00000518662.5	n.695-23786C>A		intron_variant, non_coding_transcript_variant		2
PENK-AS1	ENST00000685796.1	n.658-23786C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67587 AN: 151744 Hom.: 15286 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.446 AC: 67655 AN: 151862 Hom.: 15313 Cov.: 31 AF XY: 0.446 AC XY: 33115 AN XY: 74206

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.435

Alfa AF: 0.444 Hom.: 1899

Bravo AF: 0.438

Asia WGS AF: 0.385 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.047
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2670029; hg19: chr8-57384996;