3-191489847-C-T

Variant names:

• chr3-191489847-C-T
• rs4234621
• ENST00000439804.6:n.80+64243C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439804.6(PYDC2-AS1):​n.80+64243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,838 control chromosomes in the GnomAD database, including 18,699 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 0.48 (18699 hom., cov: 31)
• Consequence: PYDC2-AS1 ENST00000439804.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

Genes affected

PYDC2-AS1 (HGNC:52874): (PYDC2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1	n.82-56204C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYDC2-AS1	ENST00000439804.6	n.80+64243C>T		intron_variant	Intron 1 of 4	2
PYDC2-AS1	ENST00000641055.1	n.215+16159C>T		intron_variant	Intron 2 of 6
PYDC2-AS1	ENST00000641158.1	n.79+64243C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73257 AN: 151718 Hom.: 18674 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.483 AC: 73333 AN: 151838 Hom.: 18699 Cov.: 31 AF XY: 0.489 AC XY: 36280 AN XY: 74200

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.443

Alfa AF: 0.399 Hom.: 16449

Bravo AF: 0.495

Asia WGS AF: 0.586 AC: 2031 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4234621; hg19: chr3-191207636;