ENST00000438488.1:n.299-1652C>T

Variant names:

• chr3-191571662-C-T
• rs4074485
• ENST00000438488.1:n.299-1652C>T

Variant summary

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

The ENST00000438488.1(PYDC2-AS1):​n.299-1652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,216 control chromosomes in the GnomAD database, including 701 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 0.051 (701 hom., cov: 33)
• Consequence: PYDC2-AS1 ENST00000438488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1	n.568-1652C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYDC2-AS1	ENST00000438488.1	n.299-1652C>T		intron_variant	Intron 2 of 2	5
PYDC2-AS1	ENST00000439804.6	n.429-1652C>T		intron_variant	Intron 3 of 4	2
PYDC2-AS1	ENST00000641055.1	n.637-1652C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7722 AN: 152098 Hom.: 703 Cov.: 33

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0508 AC: 7729 AN: 152216 Hom.: 701 Cov.: 33 AF XY: 0.0581 AC XY: 4320 AN XY: 74412

African (AFR) AF: 0.0101 AC: 418 AN: 41570

American (AMR) AF: 0.0767 AC: 1171 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.452 AC: 2334 AN: 5164

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4826

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0327 AC: 2226 AN: 68002

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0396 Hom.: 762

Bravo AF: 0.0511

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4074485; hg19: chr3-191289451;