Genetic Variant LMO7:c.-739C>T (chr13-75760682-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_015842.2(LMO7):c.-739C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,516,842 control chromosomes in the GnomAD database, including 175,108 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 19603 hom., cov: 31)

Exomes 𝑓: 0.47 ( 155505 hom. )

Consequence

LMO7
NM_015842.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.615

Publications

15 publications found

Variant links:

Genes affected

LMO7 (HGNC:6646): (LIM domain 7) This gene encodes a protein containing a calponin homology (CH) domain, a PDZ domain, and a LIM domain, and may be involved in protein-protein interactions. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene, however, the full-length nature of some variants is not known. [provided by RefSeq, Jan 2009]

LMO7 links:

ENSG00000261553 (HGNC:):

ENSG00000261553 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015842.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LMO7	NM_001306080.2	MANE Select	c.211-250C>T	intron	N/A	NP_001293009.1	F8WD26
LMO7	NM_015842.2		c.-739C>T	5_prime_UTR	Exon 1 of 27	NP_056667.2	Q8WWI1
LMO7	NM_001366633.2		c.85-250C>T	intron	N/A	NP_001353562.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LMO7	ENST00000465261.6	TSL:1	c.-739C>T	5_prime_UTR	Exon 1 of 27	ENSP00000433352.1	A0A0A0MTE2
LMO7	ENST00000377534.8	TSL:1 MANE Select	c.211-250C>T	intron	N/A	ENSP00000366757.4	F8WD26
LMO7	ENST00000341547.8	TSL:1	c.367-250C>T	intron	N/A	ENSP00000342112.4	Q8WWI1-3

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

75943

AN:

151694

Hom.:

19602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.480

GnomAD4 exome

AF:

0.470

AC:

641562

AN:

1365032

Hom.:

155505

Cov.:

AF XY:

0.467

AC XY:

313298

AN XY:

671480

show subpopulations

African (AFR)

AF:

0.520

AC:

16043

AN:

30864

American (AMR)

AF:

0.643

AC:

21554

AN:

33522

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

9209

AN:

24206

East Asian (EAS)

AF:

0.866

AC:

30715

AN:

35468

South Asian (SAS)

AF:

0.411

AC:

31471

AN:

76530

European-Finnish (FIN)

AF:

0.544

AC:

17969

AN:

33058

Middle Eastern (MID)

AF:

0.357

AC:

1989

AN:

5574

European-Non Finnish (NFE)

AF:

0.455

AC:

485938

AN:

1068786

Other (OTH)

AF:

0.468

AC:

26674

AN:

57024

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

17476

34953

52429

69906

87382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14920

29840

44760

59680

74600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.501

AC:

75988

AN:

151810

Hom.:

19603

Cov.:

AF XY:

0.506

AC XY:

37530

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.517

AC:

21382

AN:

41366

American (AMR)

AF:

0.559

AC:

8518

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1326

AN:

3472

East Asian (EAS)

AF:

0.865

AC:

4462

AN:

5158

South Asian (SAS)

AF:

0.434

AC:

2087

AN:

4814

European-Finnish (FIN)

AF:

0.537

AC:

5657

AN:

10544

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.458

AC:

31118

AN:

67898

Other (OTH)

AF:

0.482

AC:

1018

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1900

3801

5701

7602

9502

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.466

Hom.:

21175

Bravo

AF:

0.505

Asia WGS

AF:

0.630

AC:

2188

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.92

PhyloP100

0.61

PromoterAI

0.050

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over