rs1416404046

Variant names:

• chr17-32021297-C-A
• ENST00000341671.12:c.151C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-32021297-C-A
• chr17-32021297-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_052888.3(LRRC37B):​c.151C>A​(p.Arg51Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,174 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R51C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: LRRC37B NM_052888.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

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=0.07367599).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37B	NM_001321350.2	c.1-96C>A		intron_variant	Intron 3 of 14	ENST00000543378.7	NP_001308279.1
LRRC37B	NM_052888.3	c.151C>A	p.Arg51Ser	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.1-96C>A		intron_variant	Intron 3 of 14	2	NM_001321350.2	ENSP00000443345.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461174 Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2 AN XY: 726880

Gnomad4 AFR exome AF: 0.00

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	2.7
DANN	Benign	0.83
DEOGEN2	Benign	0.013	.;T;T;T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.028	N
LIST_S2	Benign	0.15	T;T;T;.
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.074	T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.7	.;.;L;L
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.91	N;.;N;N
REVEL	Benign	0.022
Sift	Benign	0.22	T;.;T;T
Sift4G	Benign	0.74	T;T;T;T
Polyphen		0.92	.;.;P;P
Vest4		0.18
MutPred		0.31		.;.;Gain of glycosylation at R51 (P = 0.003);Gain of glycosylation at R51 (P = 0.003);
MVP		0.16
MPC		0.052
ClinPred		0.039	T
GERP RS		1.2
Varity_R		0.075
gMVP		0.084

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-30348316;