rs6035126

Variant names:

• chr20-1948896-C-T
• rs6035126
• ENST00000446562.1:n.406+1245C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446562.1(PDYN-AS1):​n.406+1245C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,064 control chromosomes in the GnomAD database, including 3,006 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 0.14 (3006 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.442+1245C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.406+1245C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21179 AN: 151946 Hom.: 2994 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.140 AC: 21233 AN: 152064 Hom.: 3006 Cov.: 32 AF XY: 0.136 AC XY: 10084 AN XY: 74358

African (AFR) AF: 0.363 AC: 15032 AN: 41402

American (AMR) AF: 0.0865 AC: 1323 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3466

East Asian (EAS) AF: 0.0208 AC: 108 AN: 5184

South Asian (SAS) AF: 0.0319 AC: 154 AN: 4822

European-Finnish (FIN) AF: 0.0394 AC: 417 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0492 AC: 3343 AN: 67994

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.0759 Hom.: 1671

Bravo AF: 0.156

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6035126; hg19: chr20-1929542;