rs6081597

Variant names:

• chr20-2014888-A-G
• rs6081597
• ENST00000651021.1:n.476-13712A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651021.1(PDYN-AS1):​n.476-13712A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• 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=-0.63).
• 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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 310 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000651021.1	n.476-13712A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00758 AC: 289 AN: 38136

American (AMR) AF: 0.0450 AC: 608 AN: 13510

Ashkenazi Jewish (ASJ) AF: 0.0546 AC: 146 AN: 2672

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0173 AC: 74 AN: 4274

European-Finnish (FIN) AF: 0.00600 AC: 61 AN: 10170

Middle Eastern (MID) AF: 0.0606 AC: 12 AN: 198

European-Non Finnish (NFE) AF: 0.0452 AC: 2727 AN: 60346

Other (OTH) AF: 0.0471 AC: 86 AN: 1824

Alfa AF: 0.0343 Hom.: 869

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6081597; hg19: chr20-1995534;