chr8-56505365-T-G

Variant names:

• chr8-56505365-T-G
• rs1440747
• ENST00000518662.5:n.827+9010T>G

Variant summary

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

The ENST00000518662.5(PENK-AS1):​n.827+9010T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,104 control chromosomes in the GnomAD database, including 52,097 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 0.82 (52097 hom., cov: 32)
• Consequence: PENK-AS1 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 3 publications found

Genes affected

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

LINC00968 (HGNC:48727): (long intergenic non-protein coding RNA 968)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PENK-AS1	NR_125813.1	n.827+9010T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PENK-AS1	ENST00000518662.5	n.827+9010T>G		intron_variant	Intron 2 of 3	2
LINC00968	ENST00000519144.5	n.477-9032A>C		intron_variant	Intron 2 of 2	4
PENK-AS1	ENST00000522511.1	n.286+9010T>G		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125280 AN: 151986 Hom.: 52041 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.824 AC: 125398 AN: 152104 Hom.: 52097 Cov.: 32 AF XY: 0.824 AC XY: 61295 AN XY: 74350

African (AFR) AF: 0.930 AC: 38591 AN: 41512

American (AMR) AF: 0.826 AC: 12612 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4492 AN: 5170

South Asian (SAS) AF: 0.857 AC: 4123 AN: 4812

European-Finnish (FIN) AF: 0.799 AC: 8452 AN: 10578

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51659 AN: 67974

Other (OTH) AF: 0.817 AC: 1726 AN: 2112

Alfa AF: 0.804 Hom.: 8646

Bravo AF: 0.830

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1440747; hg19: chr8-57417924;