20-1977499-A-G

Variant names:

• chr20-1977499-A-G
• rs6132153
• ENST00000446562.1:n.1216+11156A>G

Variant summary

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

The ENST00000446562.1(PDYN-AS1):​n.1216+11156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,170 control chromosomes in the GnomAD database, including 4,618 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 0.21 (4618 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.1252+11156A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1216+11156A>G		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.475+11156A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31332 AN: 152052 Hom.: 4616 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.206 AC: 31363 AN: 152170 Hom.: 4618 Cov.: 32 AF XY: 0.216 AC XY: 16098 AN XY: 74398

African (AFR) AF: 0.190 AC: 7900 AN: 41508

American (AMR) AF: 0.224 AC: 3422 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4336 AN: 5158

South Asian (SAS) AF: 0.462 AC: 2228 AN: 4824

European-Finnish (FIN) AF: 0.202 AC: 2141 AN: 10598

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10212 AN: 68004

Other (OTH) AF: 0.181 AC: 383 AN: 2112

Alfa AF: 0.174 Hom.: 9188

Bravo AF: 0.205

Asia WGS AF: 0.633 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.60
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs6132153; hg19: chr20-1958145;