chr20-1996802-A-G

Position:

• chr20-1996802-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134520.1(PDYN-AS1):​n.1253-10130A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 147,904 control chromosomes in the GnomAD database, including 2,374 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 0.14 (2374 hom., cov: 29)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

PDYN-AS1 (HGNC:53462): (PDYN antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.1253-10130A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000651021.1	n.475+30459A>G		intron_variant, non_coding_transcript_variant
PDYN-AS1	ENST00000446562.1	n.1217-10130A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20261 AN: 147796 Hom.: 2376 Cov.: 29

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.137 AC: 20255 AN: 147904 Hom.: 2374 Cov.: 29 AF XY: 0.146 AC XY: 10536 AN XY: 72104

Gnomad4 AFR AF: 0.0773

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.141

Alfa AF: 0.236 Hom.: 306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.23
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6045935; hg19: chr20-1977448;