rs2156892

Variant names:

• chr22-21956490-G-C
• rs2156892
• ENST00000458178.2:n.16710G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-21956490-G-C
• chr22-21956490-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000458178.2(PPM1F-AS1):​n.16710G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0046 (0 hom., cov: 24)
  • Exomes 𝑓: 0.00097 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PPM1F-AS1 ENST00000458178.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 1 publications found

Genes affected

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

ENSG00000309998 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458178.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1F-AS1	ENST00000458178.2	TSL:1	n.16710G>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309998	ENST00000846493.1		n.-149C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.00449 AC: 581 AN: 129296 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00356

Gnomad ASJ AF: 0.000631

Gnomad EAS AF: 0.000909

Gnomad SAS AF: 0.000703

Gnomad FIN AF: 0.00324

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000637

Gnomad OTH AF: 0.00167

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000969 AC: 1 AN: 1032 Hom.: 0 Cov.: 0 AF XY: 0.00186 AC XY: 1 AN XY: 538

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 86

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 28

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 838

Other (OTH) AF: 0.00 AC: 0 AN: 40

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00455 AC: 589 AN: 129358 Hom.: 0 Cov.: 24 AF XY: 0.00470 AC XY: 296 AN XY: 62970

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0147 AC: 463 AN: 31482

American (AMR) AF: 0.00356 AC: 46 AN: 12936

Ashkenazi Jewish (ASJ) AF: 0.000631 AC: 2 AN: 3172

East Asian (EAS) AF: 0.000911 AC: 4 AN: 4390

South Asian (SAS) AF: 0.000705 AC: 3 AN: 4256

European-Finnish (FIN) AF: 0.00324 AC: 29 AN: 8938

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.000637 AC: 39 AN: 61246

Other (OTH) AF: 0.00166 AC: 3 AN: 1806

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00247 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2156892; hg19: chr22-22310862;