ENST00000518662.5:n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant names:

• chr8-56448616-GTGTGTGTGTGTGTGTGTGTGTGTT-TGTGTGTGTGTGTGTGTGTGTGTGTG
• rs3219515
• ENST00000518662.5:n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000518662.5(PENK-AS1):​n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: PENK-AS1 ENST00000518662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	NR_125813.1		n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PENK-AS1	ENST00000518662.5	TSL:2	n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG		intron	N/A
	PENK-AS1	ENST00000662661.1		n.264+2116_264+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG		intron	N/A
	PENK-AS1	ENST00000685796.1		n.657+2116_657+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTGTGTG		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs3219515; hg19: chr8-57361175;