rs6444558

chr3-191557710-C-A

Variant summary

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

The NR_120606.1(PYDC2-AS1):n.265+326C>A 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 0.485 in 151,928 control chromosomes in the GnomAD database, including 19,690 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 0.49 (19690 hom., cov: 32)
• Consequence: PYDC2-AS1 NR_120606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PYDC2-AS1	NR_120606.1	n.265+326C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PYDC2-AS1	ENST00000641158.1	n.80-11890C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73587 AN: 151810 Hom.: 19642 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.485 AC: 73693 AN: 151928 Hom.: 19690 Cov.: 32 AF XY: 0.482 AC XY: 35750 AN XY: 74238

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.441

Alfa AF: 0.423 Hom.: 9953

Bravo AF: 0.494

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.6
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6444558; hg19: chr3-191275499;