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GeneBe

19-45385704-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_006663.4(PPP1R13L):c.2106G>A(p.Ser702=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000983 in 1,611,664 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 9 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 5 hom. )

Consequence

PPP1R13L
NM_006663.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.21
Variant links:
Genes affected
PPP1R13L (HGNC:18838): (protein phosphatase 1 regulatory subunit 13 like) IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.39).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-45385704-C-T is Benign according to our data. Variant chr19-45385704-C-T is described in ClinVar as [Benign]. Clinvar id is 783845.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.21 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00521 (794/152312) while in subpopulation AFR AF= 0.0182 (757/41574). AF 95% confidence interval is 0.0171. There are 9 homozygotes in gnomad4. There are 381 alleles in male gnomad4 subpopulation. Median coverage is 32. 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 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPP1R13LNM_006663.4 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 11/13 ENST00000360957.10
PPP1R13LNM_001142502.2 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 11/13
PPP1R13LXM_017026177.2 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 12/14
PPP1R13LXM_017026178.2 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 12/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPP1R13LENST00000360957.10 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 11/131 NM_006663.4 P1
PPP1R13LENST00000418234.6 linkuse as main transcriptc.2106G>A p.Ser702= synonymous_variant 11/131 P1
PPP1R13LENST00000587270.5 linkuse as main transcriptn.1579G>A non_coding_transcript_exon_variant 4/61
PPP1R13LENST00000589858.1 linkuse as main transcriptn.305G>A non_coding_transcript_exon_variant 2/32

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00518
AC:
789
AN:
152194
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0181
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00183
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00148
AC:
368
AN:
247902
Hom.:
2
AF XY:
0.00113
AC XY:
152
AN XY:
134668
show subpopulations
Gnomad AFR exome
AF:
0.0197
Gnomad AMR exome
AF:
0.00131
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000328
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000180
Gnomad OTH exome
AF:
0.000826
GnomAD4 exome
AF:
0.000541
AC:
790
AN:
1459352
Hom.:
5
Cov.:
32
AF XY:
0.000488
AC XY:
354
AN XY:
725800
show subpopulations
Gnomad4 AFR exome
AF:
0.0185
Gnomad4 AMR exome
AF:
0.00146
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000171
Gnomad4 OTH exome
AF:
0.00129
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00521
AC:
794
AN:
152312
Hom.:
9
Cov.:
32
AF XY:
0.00512
AC XY:
381
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0182
Gnomad4 AMR
AF:
0.00183
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00234
Hom.:
2
Bravo
AF:
0.00578
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
Cadd
Benign
5.8
Dann
Benign
0.95

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs35566234; hg19: chr19-45888962; API