Variant 7-123661886-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_207163.3(LMOD2):c.300A>G(p.Glu100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,533,068 control chromosomes in the GnomAD database, including 174,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 16217 hom., cov: 31)

Exomes 𝑓: 0.47 ( 158056 hom. )

Consequence

LMOD2
NM_207163.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.282

Variant links:

Genes affected

LMOD2 (HGNC:6648): (leiomodin 2) Enables actin monomer binding activity and tropomyosin binding activity. Involved in actin nucleation; positive regulation of actin filament polymerization; and sarcomere organization. Located in actin filament and sarcomere. Colocalizes with M band. [provided by Alliance of Genome Resources, Apr 2022]

LMOD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 7-123661886-A-G is Benign according to our data. Variant chr7-123661886-A-G is described in ClinVar as [Benign]. Clinvar id is 1263755.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.282 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMOD2	NM_207163.3 linkuse as main transcript	c.300A>G	p.Glu100=	synonymous_variant	2/3	ENST00000458573.3	NP_997046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMOD2	ENST00000458573.3 linkuse as main transcript	c.300A>G	p.Glu100=	synonymous_variant	2/3	2	NM_207163.3	ENSP00000411932	P1	Q6P5Q4-1
LMOD2	ENST00000456238.2 linkuse as main transcript	c.274-1153A>G		intron_variant		1		ENSP00000398975

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

69646

AN:

151904

Hom.:

16214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.602

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.475

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.481

GnomAD3 exomes

AF:

0.498

AC:

72963

AN:

146576

Hom.:

18532

AF XY:

0.510

AC XY:

39081

AN XY:

76604

show subpopulations

Gnomad AFR exome

AF:

0.398

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.528

Gnomad EAS exome

AF:

0.544

Gnomad SAS exome

AF:

0.659

Gnomad FIN exome

AF:

0.477

Gnomad NFE exome

AF:

0.464

Gnomad OTH exome

AF:

0.484

GnomAD4 exome

AF:

0.475

AC:

655960

AN:

1381046

Hom.:

158056

Cov.:

AF XY:

0.481

AC XY:

326855

AN XY:

679890

show subpopulations

Gnomad4 AFR exome

AF:

0.403

Gnomad4 AMR exome

AF:

0.461

Gnomad4 ASJ exome

AF:

0.516

Gnomad4 EAS exome

AF:

0.564

Gnomad4 SAS exome

AF:

0.655

Gnomad4 FIN exome

AF:

0.468

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.485

GnomAD4 genome

AF:

0.458

AC:

69672

AN:

152022

Hom.:

16217

Cov.:

AF XY:

0.463

AC XY:

34367

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.405

Gnomad4 AMR

AF:

0.464

Gnomad4 ASJ

AF:

0.508

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.665

Gnomad4 FIN

AF:

0.475

Gnomad4 NFE

AF:

0.460

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.466

Hom.:

32517

Bravo

AF:

0.453

Asia WGS

AF:

0.588

AC:

2045

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

5.6

DANN

Benign

0.69

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