rs7272891

Positions:

• chr20-1996172-C-G
• chr20-1996172-C-T

Variant summary

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

The NR_134520.1(PDYN-AS1):​n.1253-10760C>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 0.0865 in 152,190 control chromosomes in the GnomAD database, including 660 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 0.087 (660 hom., cov: 32)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

PDYN-AS1 (HGNC:53462): (PDYN antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.1253-10760C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000651021.1	n.475+29829C>G		intron_variant, non_coding_transcript_variant
PDYN-AS1	ENST00000446562.1	n.1217-10760C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13155 AN: 152072 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0865 AC: 13169 AN: 152190 Hom.: 660 Cov.: 32 AF XY: 0.0881 AC XY: 6557 AN XY: 74410

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0400

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.0768

Alfa AF: 0.0419 Hom.: 34

Bravo AF: 0.0898

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.74
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7272891; hg19: chr20-1976818;