20-1995366-T-C

Position:

• chr20-1995366-T-C

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

PDYN-AS1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1	n.1253-11566T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.1217-11566T>C		intron_variant		2
PDYN-AS1	ENST00000651021.1	n.475+29023T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 455 AN: 77780 Hom.: 9 Cov.: 16 FAILED QC

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

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.00355

Gnomad4 ASJ AF: 0.00282

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.00821

Gnomad4 FIN AF: 0.00281

Gnomad4 NFE AF: 0.00374

Gnomad4 OTH AF: 0.00529

Alfa AF: 0.289 Hom.: 548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61761346; hg19: chr20-1976012;