rs12548084

chr8-56465697-C-T

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+19197C>T 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 0.0589 in 152,180 control chromosomes in the GnomAD database, including 451 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 0.059 (451 hom., cov: 32)
• Consequence: PENK-AS1 NR_125813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PENK-AS1	NR_125813.1	n.694+19197C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PENK-AS1	ENST00000662661.1	n.264+19197C>T		intron_variant, non_coding_transcript_variant
PENK-AS1	ENST00000518662.5	n.694+19197C>T		intron_variant, non_coding_transcript_variant		2
PENK-AS1	ENST00000685796.1	n.657+19197C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8951 AN: 152062 Hom.: 448 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0589 AC: 8965 AN: 152180 Hom.: 451 Cov.: 32 AF XY: 0.0594 AC XY: 4415 AN XY: 74388

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0774

Alfa AF: 0.0665 Hom.: 362

Bravo AF: 0.0671

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.52
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12548084; hg19: chr8-57378256;