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GeneBe

12-6981860-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005768.6(LPCAT3):c.411C>T(p.Tyr137=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,613,806 control chromosomes in the GnomAD database, including 417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.026 ( 185 hom., cov: 32)
Exomes 𝑓: 0.0039 ( 232 hom. )

Consequence

LPCAT3
NM_005768.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.217
Variant links:
Genes affected
LPCAT3 (HGNC:30244): (lysophosphatidylcholine acyltransferase 3) Enables 1-acylglycerophosphocholine O-acyltransferase activity; 1-acylglycerophosphoethanolamine O-acyltransferase activity; and 1-acylglycerophosphoserine O-acyltransferase activity. Involved in phosphatidylcholine acyl-chain remodeling; phosphatidylethanolamine acyl-chain remodeling; and phosphatidylserine acyl-chain remodeling. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 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=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-6981860-G-A is Benign according to our data. Variant chr12-6981860-G-A is described in ClinVar as [Benign]. Clinvar id is 777232.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=-0.217 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LPCAT3NM_005768.6 linkuse as main transcriptc.411C>T p.Tyr137= synonymous_variant 4/13 ENST00000261407.9
EMG1NR_135131.2 linkuse as main transcriptn.633-5922G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LPCAT3ENST00000261407.9 linkuse as main transcriptc.411C>T p.Tyr137= synonymous_variant 4/131 NM_005768.6 P1Q6P1A2-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0257
AC:
3918
AN:
152178
Hom.:
183
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0885
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00785
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0123
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000426
Gnomad OTH
AF:
0.0196
GnomAD3 exomes
AF:
0.00680
AC:
1709
AN:
251464
Hom.:
59
AF XY:
0.00506
AC XY:
688
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.0893
Gnomad AMR exome
AF:
0.00393
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00239
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000431
Gnomad OTH exome
AF:
0.00375
GnomAD4 exome
AF:
0.00385
AC:
5631
AN:
1461510
Hom.:
232
Cov.:
30
AF XY:
0.00343
AC XY:
2491
AN XY:
727078
show subpopulations
Gnomad4 AFR exome
AF:
0.0947
Gnomad4 AMR exome
AF:
0.00427
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0397
Gnomad4 SAS exome
AF:
0.000186
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000264
Gnomad4 OTH exome
AF:
0.00576
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0258
AC:
3932
AN:
152296
Hom.:
185
Cov.:
32
AF XY:
0.0257
AC XY:
1917
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0885
Gnomad4 AMR
AF:
0.00784
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0123
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000426
Gnomad4 OTH
AF:
0.0194
Alfa
AF:
0.0137
Hom.:
41
Bravo
AF:
0.0284
Asia WGS
AF:
0.0120
AC:
42
AN:
3478
EpiCase
AF:
0.000327
EpiControl
AF:
0.000711

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 testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
0.89
Dann
Benign
0.96
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs60718946; hg19: chr12-7091021; API