rs412050

Variant names:

• chr22-21953147-G-C
• rs412050
• ENST00000458178.2:n.13367G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPM1F-AS1	ENST00000458178.2	n.13367G>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
PPM1F-AS1	ENST00000846341.1	n.186+1G>C		splice_donor_variant, intron_variant	Intron 1 of 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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.233 AC: 7 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.240 AC: 9958 AN: 41526

American (AMR) AF: 0.154 AC: 2351 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.105 AC: 505 AN: 4824

European-Finnish (FIN) AF: 0.104 AC: 1108 AN: 10618

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11841 AN: 68010

Other (OTH) AF: 0.182 AC: 385 AN: 2112

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
PhyloP100		-0.082
PromoterAI		0.27	Neutral

Splicing

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

Other links and lift over

dbSNP: rs412050; hg19: chr22-22307519;