20-1959499-T-C

Position:

• chr20-1959499-T-C

Variant summary

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

The NR_134520.1(PDYN-AS1):​n.513-6105T>C 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 0.927 in 152,016 control chromosomes in the GnomAD database, including 65,431 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 0.93 (65431 hom., cov: 29)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.513-6105T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.477-6105T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140867 AN: 151898 Hom.: 65365 Cov.: 29

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.927 AC: 140993 AN: 152016 Hom.: 65431 Cov.: 29 AF XY: 0.932 AC XY: 69235 AN XY: 74316

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.927

Alfa AF: 0.911 Hom.: 12692

Bravo AF: 0.928

Asia WGS AF: 0.982 AC: 3413 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6045664; hg19: chr20-1940145;