rs277898

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016309.3(LCMT1):​c.467-613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,056 control chromosomes in the GnomAD database, including 8,659 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8659 hom., cov: 33)

Consequence

LCMT1
NM_016309.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490
Variant links:
Genes affected
LCMT1 (HGNC:17557): (leucine carboxyl methyltransferase 1) LCMT1 catalyzes the methylation of the carboxyl group of the C-terminal leucine residue (leu309) of the catalytic subunit of protein phosphatase-2A (PPP2CA; MIM 176915) (De Baere et al., 1999 [PubMed 10600115]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LCMT1NM_016309.3 linkuse as main transcriptc.467-613G>A intron_variant ENST00000399069.8 NP_057393.2 Q9UIC8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LCMT1ENST00000399069.8 linkuse as main transcriptc.467-613G>A intron_variant 1 NM_016309.3 ENSP00000382021.3 Q9UIC8-1
LCMT1ENST00000380962.9 linkuse as main transcriptn.*324-613G>A intron_variant 2 ENSP00000370349.5 H7BYF0

Frequencies

GnomAD3 genomes
AF:
0.310
AC:
47035
AN:
151938
Hom.:
8665
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.104
Gnomad AMI
AF:
0.379
Gnomad AMR
AF:
0.371
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.356
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.309
AC:
47024
AN:
152056
Hom.:
8659
Cov.:
33
AF XY:
0.312
AC XY:
23175
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.370
Gnomad4 ASJ
AF:
0.408
Gnomad4 EAS
AF:
0.502
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.356
Gnomad4 NFE
AF:
0.389
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.353
Hom.:
2523
Bravo
AF:
0.303
Asia WGS
AF:
0.414
AC:
1440
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.67
DANN
Benign
0.64

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: rs277898; hg19: chr16-25171810; API