20-1995366-T-C

Variant names:

• chr20-1995366-T-C
• rs61761346
• ENST00000446562.1:n.1217-11566T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000446562.1(PDYN-AS1):​n.1217-11566T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0059 (9 hom., cov: 16)
  • Failed GnomAD Quality Control
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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.1253-11566T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1217-11566T>C		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.475+29023T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00585 AC: 455 AN: 77780 Hom.: 9 Cov.: 16

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00355

Gnomad ASJ AF: 0.00282

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.00818

Gnomad FIN AF: 0.00281

Gnomad MID AF: 0.00581

Gnomad NFE AF: 0.00371

Gnomad OTH AF: 0.00439

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00587 AC: 457 AN: 77834 Hom.: 9 Cov.: 16 AF XY: 0.00625 AC XY: 232 AN XY: 37134

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0111 AC: 238 AN: 21346

American (AMR) AF: 0.00355 AC: 28 AN: 7896

Ashkenazi Jewish (ASJ) AF: 0.00282 AC: 6 AN: 2128

East Asian (EAS) AF: 0.0470 AC: 11 AN: 234

South Asian (SAS) AF: 0.00821 AC: 10 AN: 1218

European-Finnish (FIN) AF: 0.00281 AC: 14 AN: 4986

Middle Eastern (MID) AF: 0.00625 AC: 1 AN: 160

European-Non Finnish (NFE) AF: 0.00374 AC: 143 AN: 38278

Other (OTH) AF: 0.00529 AC: 6 AN: 1134

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.289 Hom.: 548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.57
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs61761346; hg19: chr20-1976012;