20-1959499-T-C

Variant names:

• chr20-1959499-T-C
• rs6045664
• ENST00000446562.1:n.477-6105T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446562.1(PDYN-AS1):​n.477-6105T>C variant causes a intron 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 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446562.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.513-6105T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.477-6105T>C		intron	N/A

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

African (AFR) AF: 0.961 AC: 39866 AN: 41482

American (AMR) AF: 0.941 AC: 14382 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3145 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5182 AN: 5186

South Asian (SAS) AF: 0.961 AC: 4630 AN: 4816

European-Finnish (FIN) AF: 0.951 AC: 9976 AN: 10492

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60727 AN: 67964

Other (OTH) AF: 0.927 AC: 1957 AN: 2112

Alfa AF: 0.922 Hom.: 30277

Bravo AF: 0.928

Asia WGS AF: 0.982 AC: 3413 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.90
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6045664;

hg19: chr20-1940145;