Genetic Variant LRRC37A2:p.Arg785Gln (chr17-46515066-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001006607.3(LRRC37A2):c.2354G>A(p.Arg785Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00031 ( 3 hom., cov: 5)

Exomes 𝑓: 0.00018 ( 14 hom. )

Failed GnomAD Quality Control

Consequence

LRRC37A2
NM_001006607.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.193

Variant links:

Genes affected

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRRC37A2 links:

ARL17A (HGNC:24096): (ADP ribosylation factor like GTPase 17A) Predicted to enable GTP binding activity. Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Predicted to be located in Golgi apparatus. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARL17A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014393926).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A2	NM_001006607.3 link	c.2354G>A	p.Arg785Gln	missense_variant	Exon 1 of 14	ENST00000576629.6	NP_001006608.2	A6NM11Q5YKG5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC37A2	ENST00000576629.6 link	c.2354G>A	p.Arg785Gln	missense_variant	Exon 1 of 14	5	NM_001006607.3	ENSP00000459551.1		A6NM11

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

64882

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000923

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000260

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000341

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000108

AC:

AN:

111374

Hom.:

AF XY:

0.0000856

AC XY:

AN XY:

58442

show subpopulations

Gnomad AFR exome

AF:

0.000738

Gnomad AMR exome

AF:

0.000106

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000305

Gnomad FIN exome

AF:

0.0000790

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000184

AC:

120

AN:

652988

Hom.:

Cov.:

AF XY:

0.000185

AC XY:

AN XY:

323528

show subpopulations

Gnomad4 AFR exome

AF:

0.000792

Gnomad4 AMR exome

AF:

0.000166

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00135

Gnomad4 SAS exome

AF:

0.000198

Gnomad4 FIN exome

AF:

0.0000598

Gnomad4 NFE exome

AF:

0.0000910

Gnomad4 OTH exome

AF:

0.000108

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000308

AC:

AN:

64882

Hom.:

Cov.:

AF XY:

0.000467

AC XY:

AN XY:

32106

show subpopulations

Gnomad4 AFR

AF:

0.000923

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000260

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000341

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00792

Hom.:

ExAC

AF:

0.000143

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

May 12, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2354G>A (p.R785Q) alteration is located in exon 1 (coding exon 1) of the LRRC37A2 gene. This alteration results from a G to A substitution at nucleotide position 2354, causing the arginine (R) at amino acid position 785 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.74

DANN

Benign

0.80

DEOGEN2

Benign

0.0027

T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0036

LIST_S2

Benign

0.52

.;T

M_CAP

Benign

0.0037

MetaRNN

Benign

0.014

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

N;N

PrimateAI

Benign

0.47

PROVEAN

Benign

-0.60

.;N

REVEL

Benign

0.030

Sift

Benign

0.46

.;T

Sift4G

Benign

0.24

T;T

Polyphen

0.010

B;B

Vest4

0.037

MutPred

0.34

Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);

MVP

0.014

ClinPred

0.0042

GERP RS

-1.1

Varity_R

0.017

gMVP

0.053

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over