rs1837617

Variant names:

• chr8-56505033-G-A
• rs1837617
• ENST00000518662.5:n.827+8678G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-56505033-G-A
• chr8-56505033-G-C

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+8678G>A 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 152,166 control chromosomes in the GnomAD database, including 52,117 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 (52117 hom., cov: 32)
• Consequence: PENK-AS1 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518662.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	NR_125813.1		n.827+8678G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	ENST00000518662.5	TSL:2	n.827+8678G>A		intron	N/A
	LINC00968	ENST00000519144.5	TSL:4	n.477-8700C>T		intron	N/A
	PENK-AS1	ENST00000522511.1	TSL:4	n.286+8678G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125332 AN: 152048 Hom.: 52061 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.800

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: 125450 AN: 152166 Hom.: 52117 Cov.: 32 AF XY: 0.824 AC XY: 61326 AN XY: 74386

African (AFR) AF: 0.930 AC: 38634 AN: 41556

American (AMR) AF: 0.826 AC: 12615 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4485 AN: 5164

South Asian (SAS) AF: 0.857 AC: 4131 AN: 4820

European-Finnish (FIN) AF: 0.800 AC: 8459 AN: 10578

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

European-Non Finnish (NFE) AF: 0.760 AC: 51658 AN: 67986

Other (OTH) AF: 0.817 AC: 1724 AN: 2110

Alfa AF: 0.814 Hom.: 9787

Bravo AF: 0.830

Asia WGS AF: 0.885 AC: 3075 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		0.063

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1837617;

hg19: chr8-57417592;