13-75752146-A-T

Variant names:

• chr13-75752146-A-T
• rs539514
• NM_001306080.2:c.211-8786A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306080.2(LMO7):​c.211-8786A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,678 control chromosomes in the GnomAD database, including 29,825 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 0.61 (29825 hom., cov: 30)
• Consequence: LMO7 NM_001306080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 31 publications found

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]

ENSG00000261553 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306080.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	NM_001306080.2	MANE Select	c.211-8786A>T		intron	N/A	NP_001293009.1
	LMO7	NM_005358.5		c.367-8786A>T		intron	N/A	NP_005349.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	ENST00000377534.8	TSL:1 MANE Select	c.211-8786A>T		intron	N/A	ENSP00000366757.4
	LMO7	ENST00000341547.8	TSL:1	c.367-8786A>T		intron	N/A	ENSP00000342112.4
	LMO7	ENST00000357063.7	TSL:5	c.322-8786A>T		intron	N/A	ENSP00000349571.4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93100 AN: 151562 Hom.: 29782 Cov.: 30

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.615 AC: 93208 AN: 151678 Hom.: 29825 Cov.: 30 AF XY: 0.624 AC XY: 46207 AN XY: 74106

African (AFR) AF: 0.748 AC: 30939 AN: 41374

American (AMR) AF: 0.638 AC: 9712 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1604 AN: 3464

East Asian (EAS) AF: 0.970 AC: 5015 AN: 5168

South Asian (SAS) AF: 0.672 AC: 3219 AN: 4790

European-Finnish (FIN) AF: 0.576 AC: 6026 AN: 10468

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34917 AN: 67878

Other (OTH) AF: 0.586 AC: 1232 AN: 2104

Alfa AF: 0.928 Hom.: 33612

Bravo AF: 0.623

Asia WGS AF: 0.794 AC: 2755 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.65
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs539514; hg19: chr13-76326282; COSMIC: COSV58546889;