rs11841001

chr13-75674967-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306080.2(LMO7):c.70-38215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 152,234 control chromosomes in the GnomAD database, including 756 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 0.094 (756 hom., cov: 33)
• Consequence: LMO7 NM_001306080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO7	NM_001306080.2	c.70-38215G>A		intron_variant		ENST00000377534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO7	ENST00000377534.8	c.70-38215G>A		intron_variant		1	NM_001306080.2	P2

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14358 AN: 152120 Hom.: 757 Cov.: 33

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.0943 AC: 14361 AN: 152234 Hom.: 756 Cov.: 33 AF XY: 0.0941 AC XY: 7003 AN XY: 74436

Gnomad4 AFR AF: 0.0806

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0248

Gnomad4 SAS AF: 0.0905

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.106 Hom.: 1106

Bravo AF: 0.0961

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.0
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs11841001; hg19: chr13-76249103;