20-1995033-A-C

Variant names:

• chr20-1995033-A-C
• rs3830064
• ENST00000446562.1:n.1217-11899A>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.1217-11899A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,146 control chromosomes in the GnomAD database, including 4,477 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 0.22 (4477 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1	n.1253-11899A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.1217-11899A>C		intron_variant	Intron 3 of 3	2
PDYN-AS1	ENST00000651021.1	n.475+28690A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32910 AN: 152028 Hom.: 4474 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.217 AC: 32949 AN: 152146 Hom.: 4477 Cov.: 32 AF XY: 0.222 AC XY: 16526 AN XY: 74380

African (AFR) AF: 0.282 AC: 11685 AN: 41490

American (AMR) AF: 0.127 AC: 1945 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3555 AN: 5170

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4820

European-Finnish (FIN) AF: 0.203 AC: 2154 AN: 10596

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10526 AN: 67988

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.164 Hom.: 3922

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs3830064; hg19: chr20-1975679;