chr17-32021159-C-A

Variant summary

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

The NM_052888.3(LRRC37B):​c.13C>A​(p.Arg5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R5C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

LRRC37B
NM_052888.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.959
Variant links:
Genes affected
LRRC37B (HGNC:29070): (leucine rich repeat containing 37B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.0844976).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRRC37BNM_001321350.2 linkc.1-234C>A intron_variant Intron 3 of 14 ENST00000543378.7 NP_001308279.1 F5H5K1B4DSJ3B4DZ43
LRRC37BNM_052888.3 linkc.13C>A p.Arg5Ser missense_variant Exon 1 of 12 NP_443120.2 Q96QE4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LRRC37BENST00000543378.7 linkc.1-234C>A intron_variant Intron 3 of 14 2 NM_001321350.2 ENSP00000443345.2 F5H5K1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
0.37
DANN
Benign
0.85
DEOGEN2
Benign
0.036
.;T;T;T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.0089
N
LIST_S2
Benign
0.75
T;T;T;.
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.084
T;T;T;T
MetaSVM
Benign
-0.86
T
MutationAssessor
Uncertain
2.3
.;.;M;M
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.7
N;.;N;N
REVEL
Benign
0.10
Sift
Uncertain
0.0030
D;.;D;D
Sift4G
Benign
0.43
T;T;T;T
Polyphen
0.96
.;.;D;D
Vest4
0.094
MutPred
0.42
.;.;Loss of MoRF binding (P = 2e-04);Loss of MoRF binding (P = 2e-04);
MVP
0.13
MPC
0.11
ClinPred
0.078
T
GERP RS
-1.6
Varity_R
0.10
gMVP
0.13

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: rs919864891; hg19: chr17-30348178; API