rs11841001

Variant names:

• chr13-75674967-G-A
• rs11841001
• NM_001306080.2:c.70-38215G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 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.70-38215G>A		intron	N/A	NP_001293009.1
	LMO7	NM_005358.5		c.226-38215G>A		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.70-38215G>A		intron	N/A	ENSP00000366757.4
	LMO7	ENST00000341547.8	TSL:1	c.226-38215G>A		intron	N/A	ENSP00000342112.4
	LMO7	ENST00000357063.7	TSL:5	c.181-38215G>A		intron	N/A	ENSP00000349571.4

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

African (AFR) AF: 0.0806 AC: 3349 AN: 41548

American (AMR) AF: 0.0984 AC: 1504 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3472

East Asian (EAS) AF: 0.0248 AC: 129 AN: 5194

South Asian (SAS) AF: 0.0905 AC: 436 AN: 4820

European-Finnish (FIN) AF: 0.0736 AC: 779 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7333 AN: 68002

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.105 Hom.: 1520

Bravo AF: 0.0961

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.74
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11841001; hg19: chr13-76249103;