chr17-32021159-C-A

Variant names:

• chr17-32021159-C-A
• rs919864891
• ENST00000341671.12:c.13C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

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]

ACMG classification

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
LRRC37B	NM_001321350.2	c.1-234C>A		intron_variant	Intron 3 of 14	ENST00000543378.7	NP_001308279.1
LRRC37B	NM_052888.3	c.13C>A	p.Arg5Ser	missense_variant	Exon 1 of 12		NP_443120.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC37B	ENST00000543378.7	c.1-234C>A		intron_variant	Intron 3 of 14	2	NM_001321350.2	ENSP00000443345.2

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

Other links and lift over

dbSNP: rs919864891; hg19: chr17-30348178;