rs16822582

Variant names:

• chr3-191478803-A-G
• rs16822582
• ENST00000439804.6:n.80+53199A>G

Variant summary

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

The ENST00000439804.6(PYDC2-AS1):​n.80+53199A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,298 control chromosomes in the GnomAD database, including 217 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 0.049 (217 hom., cov: 33)
• Consequence: PYDC2-AS1 ENST00000439804.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 0 publications found

Genes affected

PYDC2-AS1 (HGNC:52874): (PYDC2 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 (EAS) allele frequency at 95% confidence interval = 0.089 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439804.6. 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
	PYDC2-AS1	NR_120606.1		n.81+53199A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYDC2-AS1	ENST00000439804.6	TSL:2	n.80+53199A>G		intron	N/A
	PYDC2-AS1	ENST00000641055.1		n.215+5115A>G		intron	N/A
	PYDC2-AS1	ENST00000641158.1		n.79+53199A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7460 AN: 152180 Hom.: 217 Cov.: 33

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0348

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0490 AC: 7468 AN: 152298 Hom.: 217 Cov.: 33 AF XY: 0.0472 AC XY: 3514 AN XY: 74480

African (AFR) AF: 0.0407 AC: 1691 AN: 41568

American (AMR) AF: 0.0348 AC: 532 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3472

East Asian (EAS) AF: 0.0959 AC: 498 AN: 5192

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4832

European-Finnish (FIN) AF: 0.0238 AC: 252 AN: 10602

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4188 AN: 68024

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0528 Hom.: 238

Bravo AF: 0.0483

Asia WGS AF: 0.0650 AC: 224 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	1.4
DANN	Benign	0.20
PhyloP100		0.11

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: rs16822582;

hg19: chr3-191196592;