Variant chr20-1994400-A-AAG details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000446562.1(PDYN-AS1):n.1217-12514_1217-12513dupGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000605 in 150,470 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00060 ( 1 hom., cov: 30)

Exomes 𝑓: 0.0068 ( 0 hom. )

Consequence

PDYN-AS1
ENST00000446562.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.590

Variant links:

Genes affected

PDYN-AS1 (HGNC:):

PDYN-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
PDYN-AS1	NR_134520.1 linkuse as main transcript	n.1253-12514_1253-12513dupGA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1 linkuse as main transcript	n.1217-12514_1217-12513dupGA		intron_variant		2
PDYN-AS1	ENST00000651021.1 linkuse as main transcript	n.475+28075_475+28076dupGA		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.000599

AC:

AN:

150226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000512

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00105

Gnomad FIN

AF:

0.00533

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000149

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00685

AC:

AN:

146

Hom.:

AF XY:

0.00980

AC XY:

AN XY:

102

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0111

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.000599

AC:

AN:

150324

Hom.:

Cov.:

AF XY:

0.000913

AC XY:

AN XY:

73380

show subpopulations

Gnomad4 AFR

AF:

0.000511

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00106

Gnomad4 FIN

AF:

0.00533

Gnomad4 NFE

AF:

0.000149

Gnomad4 OTH

AF:

0.00

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over