rs780641230

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_016027.3(LACTB2):​c.340A>T​(p.Ile114Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

LACTB2
NM_016027.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.43
Variant links:
Genes affected
LACTB2 (HGNC:18512): (lactamase beta 2) Enables endoribonuclease activity; single-stranded RNA binding activity; and zinc ion binding activity. Involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
LACTB2-AS1 (HGNC:27841): (LACTB2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25043228).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LACTB2NM_016027.3 linkc.340A>T p.Ile114Leu missense_variant Exon 3 of 7 ENST00000276590.5 NP_057111.1 Q53H82A0A024R811
LACTB2-AS1NR_038881.1 linkn.582-2316T>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LACTB2ENST00000276590.5 linkc.340A>T p.Ile114Leu missense_variant Exon 3 of 7 1 NM_016027.3 ENSP00000276590.4 Q53H82
LACTB2-AS1ENST00000499227.6 linkn.582-2316T>A intron_variant Intron 3 of 3 1
LACTB2ENST00000522447.5 linkc.340A>T p.Ile114Leu missense_variant Exon 3 of 8 2 ENSP00000428801.1 Q53H82

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1459082
Hom.:
0
Cov.:
28
AF XY:
0.00000275
AC XY:
2
AN XY:
726080
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.01e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.098
BayesDel_addAF
Uncertain
0.043
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
19
DANN
Benign
0.96
DEOGEN2
Benign
0.21
T;T
Eigen
Benign
-0.31
Eigen_PC
Benign
-0.11
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Benign
0.63
.;T
M_CAP
Benign
0.051
D
MetaRNN
Benign
0.25
T;T
MetaSVM
Benign
-0.78
T
MutationAssessor
Benign
1.4
L;L
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-0.77
N;N
REVEL
Benign
0.24
Sift
Benign
0.54
T;T
Sift4G
Benign
0.65
T;T
Polyphen
0.0050
B;B
Vest4
0.46
MutPred
0.49
Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
0.60
MPC
0.027
ClinPred
0.74
D
GERP RS
4.6
Varity_R
0.23
gMVP
0.71

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: rs780641230; hg19: chr8-71570064; API