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2-28751664-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The XR_007086259.1(PPP1CB-DT):n.93T>G 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 0.0123 in 184,138 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.014 ( 47 hom., cov: 31)
Exomes 𝑓: 0.0031 ( 0 hom. )

Consequence

PPP1CB-DT
XR_007086259.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.84
Variant links:
Genes affected
PPP1CB-DT (HGNC:55829): (PPP1CB divergent transcript)
PPP1CB (HGNC:9282): (protein phosphatase 1 catalytic subunit beta) The protein encoded by this gene is one of the three catalytic subunits of protein phosphatase 1 (PP1). PP1 is a serine/threonine specific protein phosphatase known to be involved in the regulation of a variety of cellular processes, such as cell division, glycogen metabolism, muscle contractility, protein synthesis, and HIV-1 viral transcription. Mouse studies suggest that PP1 functions as a suppressor of learning and memory. Two alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-28751664-A-C is Benign according to our data. Variant chr2-28751664-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1191835.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0142 (2169/152302) while in subpopulation AFR AF= 0.0403 (1675/41580). AF 95% confidence interval is 0.0387. There are 47 homozygotes in gnomad4. There are 1098 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 47 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPP1CB-DTXR_007086259.1 linkuse as main transcriptn.93T>G non_coding_transcript_exon_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPP1CBENST00000455580.6 linkuse as main transcriptc.-189A>C 5_prime_UTR_variant 1/83
PPP1CB-DTENST00000653462.1 linkuse as main transcriptn.59T>G non_coding_transcript_exon_variant 1/4
PPP1CBENST00000420282.6 linkuse as main transcript upstream_gene_variant 4 P1
PPP1CB-DTENST00000665023.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0143
AC:
2171
AN:
152194
Hom.:
47
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0404
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00497
Gnomad ASJ
AF:
0.00576
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00393
Gnomad FIN
AF:
0.0197
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00231
Gnomad OTH
AF:
0.00622
GnomAD4 exome
AF:
0.00308
AC:
98
AN:
31836
Hom.:
0
Cov.:
0
AF XY:
0.00223
AC XY:
40
AN XY:
17920
show subpopulations
Gnomad4 AFR exome
AF:
0.0469
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00148
Gnomad4 FIN exome
AF:
0.0104
Gnomad4 NFE exome
AF:
0.00224
Gnomad4 OTH exome
AF:
0.00788
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0142
AC:
2169
AN:
152302
Hom.:
47
Cov.:
31
AF XY:
0.0147
AC XY:
1098
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0403
Gnomad4 AMR
AF:
0.00490
Gnomad4 ASJ
AF:
0.00576
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.0197
Gnomad4 NFE
AF:
0.00231
Gnomad4 OTH
AF:
0.00616
Alfa
AF:
0.00145
Hom.:
0
Bravo
AF:
0.0152
Asia WGS
AF:
0.00579
AC:
20
AN:
3470

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxFeb 21, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
0.052
Dann
Benign
0.52

Splicing

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: rs147139861; hg19: chr2-28974530; API