chr3-191472176-A-G

Position:

• chr3-191472176-A-G

Variant summary

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

The NR_120606.1(PYDC2-AS1):​n.81+46572A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,158 control chromosomes in the GnomAD database, including 1,426 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 0.12 (1426 hom., cov: 32)
• Consequence: PYDC2-AS1 NR_120606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PYDC2-AS1	NR_120606.1	n.81+46572A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PYDC2-AS1	ENST00000641158.1	n.79+46572A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18177 AN: 152040 Hom.: 1421 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.120 AC: 18186 AN: 152158 Hom.: 1426 Cov.: 32 AF XY: 0.127 AC XY: 9416 AN XY: 74376

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.127

Alfa AF: 0.129 Hom.: 2912

Bravo AF: 0.114

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2886242; hg19: chr3-191189965;