Variant rs3219515 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000518662.5(PENK-AS1):n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTG 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57

Variant links:

Genes affected

PENK-AS1 (HGNC:):

PENK-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PENK-AS1	NR_125813.1 linkuse as main transcript	n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
PENK-AS1	ENST00000518662.5 linkuse as main transcript	n.694+2116_694+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTG	intron_variant	2
PENK-AS1	ENST00000662661.1 linkuse as main transcript	n.264+2116_264+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTG	intron_variant
PENK-AS1	ENST00000685796.1 linkuse as main transcript	n.657+2116_657+2140delGTGTGTGTGTGTGTGTGTGTGTGTTinsTGTGTGTGTGTGTGTGTGTGTG	intron_variant

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.