rs6081597

Positions:

• chr20-2014888-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651021.1(PDYN-AS1):​n.476-13712A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 137,092 control chromosomes in the GnomAD database, including 310 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 0.029 (310 hom., cov: 31)
• Consequence: PDYN-AS1 ENST00000651021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0294 (4037/137092) while in subpopulation NFE AF= 0.0452 (2727/60346). AF 95% confidence interval is 0.0438. There are 310 homozygotes in gnomad4. There are 1868 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 310 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000651021.1	n.476-13712A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4037 AN: 136980 Hom.: 309 Cov.: 31

Gnomad AFR AF: 0.00760

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0546

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0173

Gnomad FIN AF: 0.00600

Gnomad MID AF: 0.0556

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0477

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

GnomAD4 genome AF: 0.0294 AC: 4037 AN: 137092 Hom.: 310 Cov.: 31 AF XY: 0.0278 AC XY: 1868 AN XY: 67260

Gnomad4 AFR AF: 0.00758

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0546

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0173

Gnomad4 FIN AF: 0.00600

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0471

Alfa AF: 0.0344 Hom.: 233

Bravo AF: 0.0287

Asia WGS AF: 0.00639 AC: 23 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6081597; hg19: chr20-1995534;