Variant 13-75623309-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005358.5(LMO7):c.214A>T(p.Ile72Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LMO7
NM_005358.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0510

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:

LMO7 (HGNC:):

LMO7 links:

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ACMG classification

Classification made for transcript

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=0.09580588).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
LMO7	NM_005358.5 linkuse as main transcript	c.214A>T	p.Ile72Phe	missense_variant	2/30	NP_005349.3
LMO7	XM_047430323.1 linkuse as main transcript	c.-642A>T		5_prime_UTR_variant	2/34	XP_047286279.1
LMO7	XM_047430329.1 linkuse as main transcript	c.-642A>T		5_prime_UTR_variant	2/33	XP_047286285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
LMO7	ENST00000341547.8 linkuse as main transcript	c.214A>T	p.Ile72Phe	missense_variant	2/30	1	ENSP00000342112.4	Q8WWI1-3
LMO7	ENST00000357063.7 linkuse as main transcript	c.169A>T	p.Ile57Phe	missense_variant	2/32	5	ENSP00000349571.4	J3KP06
LMO7	ENST00000533299.2 linkuse as main transcript	n.40A>T		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1272530

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

642702

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:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2023

The c.214A>T (p.I72F) alteration is located in exon 2 (coding exon 2) of the LMO7 gene. This alteration results from a A to T substitution at nucleotide position 214, causing the isoleucine (I) at amino acid position 72 to be replaced by a phenylalanine (F). 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

BayesDel_addAF

Benign

-0.10

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.6

DANN

Benign

0.66

DEOGEN2

Benign

0.018

T;.

Eigen

Benign

-0.94

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.43

T;T

M_CAP

Benign

0.010

MetaRNN

Benign

0.096

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Uncertain

2.2

.;M

PROVEAN

Benign

1.2

.;N

REVEL

Benign

0.064

Sift

Benign

0.040

.;D

Sift4G

Benign

0.63

T;T

Polyphen

0.092

.;B

Vest4

0.14

MVP

0.42

ClinPred

0.43

GERP RS

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over