rs12548084

Variant names:

• chr8-56465697-C-T
• rs12548084
• ENST00000518662.5:n.694+19197C>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+19197C>T variant causes a intron 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 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 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=-0.99).
• 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 rank	MANE	Protein	UniProt
PENK-AS1	NR_125813.1	n.694+19197C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PENK-AS1	ENST00000518662.5	n.694+19197C>T		intron_variant	Intron 1 of 3	2
PENK-AS1	ENST00000662661.1	n.264+19197C>T		intron_variant	Intron 1 of 4
PENK-AS1	ENST00000685796.1	n.657+19197C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0144 AC: 598 AN: 41532

American (AMR) AF: 0.121 AC: 1843 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1233 AN: 5146

South Asian (SAS) AF: 0.0762 AC: 368 AN: 4828

European-Finnish (FIN) AF: 0.0390 AC: 414 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4126 AN: 68004

Other (OTH) AF: 0.0774 AC: 163 AN: 2106

Alfa AF: 0.0636 Hom.: 588

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12548084; hg19: chr8-57378256;