rs412050

chr22-21953147-G-C

Variant summary

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

The ENST00000458178.2(PPM1F-AS1):n.13367G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,300 control chromosomes in the GnomAD database, including 2,675 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 0.18 (2674 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: PPM1F-AS1 ENST00000458178.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

PPM1F-AS1 (HGNC:40888): (PPM1F antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPM1F-AS1	ENST00000458178.2	n.13367G>C		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27066 AN: 152140 Hom.: 2672 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.238 AC: 10 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 8 AN XY: 32

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.178 AC: 27087 AN: 152258 Hom.: 2674 Cov.: 32 AF XY: 0.171 AC XY: 12738 AN XY: 74454

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.182

Alfa AF: 0.167 Hom.: 317

Bravo AF: 0.187

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.0
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412050; hg19: chr22-22307519;