rs2029721

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020700.2(PPM1H):​c.870-17978C>T variant causes a intron change. The variant allele was found at a frequency of 0.332 in 653,130 control chromosomes in the GnomAD database, including 38,593 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 0.29 ( 7471 hom., cov: 31)
Exomes 𝑓: 0.34 ( 31122 hom. )

Consequence

PPM1H
NM_020700.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.97
Variant links:
Genes affected
PPM1H (HGNC:18583): (protein phosphatase, Mg2+/Mn2+ dependent 1H) Enables identical protein binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPM1HNM_020700.2 linkuse as main transcriptc.870-17978C>T intron_variant ENST00000228705.7 NP_065751.1 Q9ULR3
PPM1HXM_011538578.3 linkuse as main transcriptc.756-17978C>T intron_variant XP_011536880.1
PPM1HXM_017019676.3 linkuse as main transcriptc.870-17978C>T intron_variant XP_016875165.1
GAPDHP44 use as main transcriptn.62755564G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPM1HENST00000228705.7 linkuse as main transcriptc.870-17978C>T intron_variant 1 NM_020700.2 ENSP00000228705.5 Q9ULR3
GAPDHP44ENST00000513513.1 linkuse as main transcriptn.338G>A non_coding_transcript_exon_variant 1/16
PPM1HENST00000551519.1 linkuse as main transcriptn.260-17978C>T intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.289
AC:
43880
AN:
151888
Hom.:
7471
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.435
Gnomad AMR
AF:
0.326
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.205
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.433
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.370
Gnomad OTH
AF:
0.305
GnomAD4 exome
AF:
0.345
AC:
172767
AN:
501124
Hom.:
31122
Cov.:
2
AF XY:
0.341
AC XY:
92932
AN XY:
272180
show subpopulations
Gnomad4 AFR exome
AF:
0.112
Gnomad4 AMR exome
AF:
0.377
Gnomad4 ASJ exome
AF:
0.275
Gnomad4 EAS exome
AF:
0.219
Gnomad4 SAS exome
AF:
0.280
Gnomad4 FIN exome
AF:
0.424
Gnomad4 NFE exome
AF:
0.376
Gnomad4 OTH exome
AF:
0.335
GnomAD4 genome
AF:
0.289
AC:
43881
AN:
152006
Hom.:
7471
Cov.:
31
AF XY:
0.289
AC XY:
21506
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.326
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.205
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.433
Gnomad4 NFE
AF:
0.370
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.342
Hom.:
1242
Bravo
AF:
0.275
Asia WGS
AF:
0.240
AC:
839
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
CADD
Benign
5.1
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2029721; hg19: chr12-63149344; API