rs1016618

chr3-191511201-T-C

Variant summary

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

The NR_120606.1(PYDC2-AS1):n.82-34850T>C 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 0.0937 in 152,246 control chromosomes in the GnomAD database, including 1,055 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 0.094 (1055 hom., cov: 32)
• Consequence: PYDC2-AS1 NR_120606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PYDC2-AS1	NR_120606.1	n.82-34850T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PYDC2-AS1	ENST00000641158.1	n.80-58399T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14263 AN: 152128 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0937 AC: 14267 AN: 152246 Hom.: 1055 Cov.: 32 AF XY: 0.0998 AC XY: 7427 AN XY: 74422

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0945

Alfa AF: 0.101 Hom.: 1660

Bravo AF: 0.0934

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016618; hg19: chr3-191228990;