12-1828174-G-A

Position:

chr12-1828174-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001039029.3(LRTM2):c.26G>A(p.Gly9Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,546,704 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., cov: 34)

Exomes 𝑓: 0.0011 ( 1 hom. )

Consequence

LRTM2
NM_001039029.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.00

Variant links:

Genes affected

LRTM2 (HGNC:32443): (leucine rich repeats and transmembrane domains 2) Predicted to enable Roundabout binding activity and heparin binding activity. Predicted to be involved in axon guidance and negative chemotaxis. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRTM2 links:

CACNA2D4 (HGNC:20202): (calcium voltage-gated channel auxiliary subunit alpha2delta 4) This gene encodes a member of the alpha-2/delta subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Various versions of each of these subunits exist, either expressed from similar genes or the result of alternative splicing. Research on a highly similar protein in rabbit suggests the protein described in this record is cleaved into alpha-2 and delta subunits. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

CACNA2D4 links:

LRTM2 (HGNC:):

LRTM2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0072345436).

BP6

Variant 12-1828174-G-A is Benign according to our data. Variant chr12-1828174-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2368694.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 76 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRTM2	NM_001039029.3 linkuse as main transcript	c.26G>A	p.Gly9Glu	missense_variant	3/5	ENST00000299194.6	NP_001034118.1	Q8N967
CACNA2D4	NM_172364.5 linkuse as main transcript	c.2551+12565C>T		intron_variant		ENST00000382722.10	NP_758952.4	Q7Z3S7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LRTM2	ENST00000299194.6 linkuse as main transcript	c.26G>A	p.Gly9Glu	missense_variant	3/5	2	NM_001039029.3	ENSP00000299194.1	Q8N967
CACNA2D4	ENST00000382722.10 linkuse as main transcript	c.2551+12565C>T		intron_variant		1	NM_172364.5	ENSP00000372169.4	Q7Z3S7-1
CACNA2D4	ENST00000586184.5 linkuse as main transcript	c.2551+12565C>T		intron_variant		5		ENSP00000465060.1	Q7Z3S7-5
CACNA2D4	ENST00000587995.5 linkuse as main transcript	c.2476+12565C>T		intron_variant		5		ENSP00000465372.1	K7EJY1
CACNA2D4	ENST00000585708.5 linkuse as main transcript	c.2359+12565C>T		intron_variant		5		ENSP00000467697.1	Q7Z3S7-6
CACNA2D4	ENST00000588077.5 linkuse as main transcript	c.2359+12565C>T		intron_variant		5		ENSP00000468530.1	Q7Z3S7-4
CACNA2D4	ENST00000444595.6 linkuse as main transcript	n.*797+12565C>T		intron_variant		1		ENSP00000403371.2	E7EUE0
CACNA2D4	ENST00000537784.5 linkuse as main transcript	n.391+12565C>T		intron_variant		1		ENSP00000440231.2	X6RLU5

Frequencies

GnomAD3 genomes

AF:

0.000499

AC:

AN:

152236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000853

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000433

AC:

AN:

145558

Hom.:

AF XY:

0.000413

AC XY:

AN XY:

77532

show subpopulations

Gnomad AFR exome

AF:

0.000267

Gnomad AMR exome

AF:

0.000294

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000448

Gnomad FIN exome

AF:

0.000264

Gnomad NFE exome

AF:

0.000875

Gnomad OTH exome

AF:

0.000482

GnomAD4 exome

AF:

0.00109

AC:

1523

AN:

1394350

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

749

AN XY:

687660

show subpopulations

Gnomad4 AFR exome

AF:

0.000287

Gnomad4 AMR exome

AF:

0.000340

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000762

Gnomad4 FIN exome

AF:

0.000230

Gnomad4 NFE exome

AF:

0.00130

Gnomad4 OTH exome

AF:

0.00138

GnomAD4 genome

AF:

0.000499

AC:

AN:

152354

Hom.:

Cov.:

AF XY:

0.000416

AC XY:

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.000853

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.000753

Hom.:

Bravo

AF:

0.000518

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.000270

AC:

ESP6500EA

AF:

0.000983

AC:

ExAC

AF:

0.000212

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 02, 2022

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.72

DEOGEN2

Benign

0.010

T;T;T;T;T

Eigen

Benign

-0.95

Eigen_PC

Benign

-0.79

FATHMM_MKL

Benign

0.034

M_CAP

Benign

0.011

MetaRNN

Benign

0.0072

T;T;T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-0.55

N;N;N;.;.

PrimateAI

Benign

0.34

PROVEAN

Benign

0.25

N;N;N;N;N

REVEL

Benign

0.17

Sift

Benign

1.0

T;T;T;T;T

Sift4G

Benign

1.0

T;T;T;T;T

Polyphen

0.0

B;B;B;.;.

Vest4

0.072

MVP

0.48

MPC

0.39

ClinPred

0.0010

GERP RS

3.2

Varity_R

0.029

gMVP

0.40

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