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GeneBe

21-14152629-C-T

Variant summary

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

The NM_001302998.2(LIPI):c.1062G>A(p.Ser354=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000392 in 1,590,702 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00027 ( 3 hom. )

Consequence

LIPI
NM_001302998.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.827
Variant links:
Genes affected
LIPI (HGNC:18821): (lipase I) The protein encoded by this gene is a phospholipase that hydrolyzes phosphatidic acid to produce lysophosphatidic acid. Defects in this gene are a cause of susceptibility to familial hypertrigliceridemia. This gene is also expressed at high levels in Ewing family tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

Genome browser will be placed here

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=-0.68).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 21-14152629-C-T is Benign according to our data. Variant chr21-14152629-C-T is described in ClinVar as [Benign]. Clinvar id is 1532871.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=0.827 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 232 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LIPINM_001302998.2 linkuse as main transcriptc.1062G>A p.Ser354= synonymous_variant 8/10 ENST00000681601.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LIPIENST00000681601.1 linkuse as main transcriptc.1062G>A p.Ser354= synonymous_variant 8/10 NM_001302998.2 P4Q6XZB0-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00153
AC:
232
AN:
151956
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00488
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00138
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.000510
AC:
127
AN:
249130
Hom.:
0
AF XY:
0.000467
AC XY:
63
AN XY:
134846
show subpopulations
Gnomad AFR exome
AF:
0.00447
Gnomad AMR exome
AF:
0.000815
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000219
Gnomad SAS exome
AF:
0.0000990
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000160
Gnomad OTH exome
AF:
0.000496
GnomAD4 exome
AF:
0.000272
AC:
391
AN:
1438628
Hom.:
3
Cov.:
27
AF XY:
0.000251
AC XY:
180
AN XY:
717078
show subpopulations
Gnomad4 AFR exome
AF:
0.00495
Gnomad4 AMR exome
AF:
0.000673
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000331
Gnomad4 SAS exome
AF:
0.0000937
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000133
Gnomad4 OTH exome
AF:
0.000470
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00153
AC:
232
AN:
152074
Hom.:
0
Cov.:
32
AF XY:
0.00152
AC XY:
113
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.00487
Gnomad4 AMR
AF:
0.00138
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.000474
Alfa
AF:
0.000878
Hom.:
0
Bravo
AF:
0.00179
Asia WGS
AF:
0.00116
AC:
4
AN:
3462
EpiCase
AF:
0.000219
EpiControl
AF:
0.000356

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 testingInvitaeMar 29, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
5.9
Dann
Benign
0.48

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: rs148202419; hg19: chr21-15524950; COSMIC: COSV100753465; API