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GeneBe

9-68917631-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_003558.4(PIP5K1B):c.855G>A(p.Glu285=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00575 in 1,613,924 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0059 ( 34 hom. )

Consequence

PIP5K1B
NM_003558.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.198
Variant links:
Genes affected
PIP5K1B (HGNC:8995): (phosphatidylinositol-4-phosphate 5-kinase type 1 beta) Predicted to enable 1-phosphatidylinositol-4-phosphate 5-kinase activity. Predicted to be involved in regulation of phosphatidylinositol 3-kinase signaling. Predicted to act upstream of or within phosphatidylinositol biosynthetic process. Located in uropod. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.7).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-68917631-G-A is Benign according to our data. Variant chr9-68917631-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3067185.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=-0.198 with no splicing effect.
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 AC in GnomAd at 634 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIP5K1BNM_003558.4 linkuse as main transcriptc.855G>A p.Glu285= synonymous_variant 9/16 ENST00000265382.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIP5K1BENST00000265382.8 linkuse as main transcriptc.855G>A p.Glu285= synonymous_variant 9/161 NM_003558.4 P1O14986-1
PIP5K1BENST00000478500.3 linkuse as main transcriptc.975G>A p.Glu325= synonymous_variant, NMD_transcript_variant 10/211 O14986-2
PIP5K1BENST00000541509.5 linkuse as main transcriptc.855G>A p.Glu285= synonymous_variant 8/142 O14986-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00417
AC:
634
AN:
152180
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.00349
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00657
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00431
AC:
1084
AN:
251336
Hom.:
6
AF XY:
0.00431
AC XY:
585
AN XY:
135820
show subpopulations
Gnomad AFR exome
AF:
0.00197
Gnomad AMR exome
AF:
0.00217
Gnomad ASJ exome
AF:
0.000893
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00389
Gnomad FIN exome
AF:
0.00333
Gnomad NFE exome
AF:
0.00665
Gnomad OTH exome
AF:
0.00343
GnomAD4 exome
AF:
0.00592
AC:
8647
AN:
1461626
Hom.:
34
Cov.:
31
AF XY:
0.00591
AC XY:
4297
AN XY:
727128
show subpopulations
Gnomad4 AFR exome
AF:
0.00185
Gnomad4 AMR exome
AF:
0.00244
Gnomad4 ASJ exome
AF:
0.000803
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00405
Gnomad4 FIN exome
AF:
0.00354
Gnomad4 NFE exome
AF:
0.00686
Gnomad4 OTH exome
AF:
0.00465
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00418
AC:
637
AN:
152298
Hom.:
1
Cov.:
32
AF XY:
0.00377
AC XY:
281
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.00176
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00270
Gnomad4 FIN
AF:
0.00349
Gnomad4 NFE
AF:
0.00657
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00560
Hom.:
0
Bravo
AF:
0.00396
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.00600
EpiControl
AF:
0.00522

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 testingCeGaT Center for Human Genetics TuebingenMar 01, 2024PIP5K1B: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
Cadd
Benign
3.8
Dann
Benign
0.44

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: rs61752951; hg19: chr9-71532547; COSMIC: COSV99600251; API