rs6035310

Variant names:

• chr20-2007953-A-C
• rs6035310
• ENST00000651021.1:n.476-20647A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-2007953-A-C
• chr20-2007953-A-T

Variant summary

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

The ENST00000651021.1(PDYN-AS1):​n.476-20647A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,158 control chromosomes in the GnomAD database, including 3,556 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 0.19 (3556 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000651021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651021.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000651021.1		n.476-20647A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29001 AN: 152040 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.191 AC: 28998 AN: 152158 Hom.: 3556 Cov.: 32 AF XY: 0.200 AC XY: 14889 AN XY: 74390

African (AFR) AF: 0.150 AC: 6241 AN: 41522

American (AMR) AF: 0.129 AC: 1971 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3420 AN: 5176

South Asian (SAS) AF: 0.423 AC: 2042 AN: 4822

European-Finnish (FIN) AF: 0.253 AC: 2676 AN: 10564

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11633 AN: 67978

Other (OTH) AF: 0.168 AC: 356 AN: 2116

Alfa AF: 0.177 Hom.: 5624

Bravo AF: 0.177

Asia WGS AF: 0.521 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.77
DANN	Benign	0.57
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6035310;

hg19: chr20-1988599;