20-1994400-AAGAGAGAGAG-AAGAGAG

Position:

• chr20-1994400-AAGAGAGAGAG-AAGAGAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000446562.1(PDYN-AS1):​n.1217-12516_1217-12513delGAGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 150,394 control chromosomes in the GnomAD database, including 1,235 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1235 hom., cov: 30)
  • Exomes 𝑓: 0.055 (0 hom.)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741

Genes affected

PDYN-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1	n.1253-12516_1253-12513delGAGA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.1217-12516_1217-12513delGAGA		intron_variant		2
PDYN-AS1	ENST00000651021.1	n.475+28073_475+28076delGAGA		intron_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 17962 AN: 150150 Hom.: 1234 Cov.: 30

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0716

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.0548 AC: 8 AN: 146 Hom.: 0 AF XY: 0.0686 AC XY: 7 AN XY: 102

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0667

Gnomad4 NFE exome AF: 0.0556

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.120 AC: 17988 AN: 150248 Hom.: 1235 Cov.: 30 AF XY: 0.123 AC XY: 9003 AN XY: 73338

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.132

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34535593; hg19: chr20-1975046;