rs1570555

Positions:

• chr13-75797740-A-G

Variant summary

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

The NM_001306080.2(LMO7):​c.462+991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,144 control chromosomes in the GnomAD database, including 3,160 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 0.18 (3160 hom., cov: 32)
• Consequence: LMO7 NM_001306080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO7	NM_001306080.2	c.462+991A>G		intron_variant		ENST00000377534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO7	ENST00000377534.8	c.462+991A>G		intron_variant		1	NM_001306080.2	P2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27625 AN: 152026 Hom.: 3161 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.181 AC: 27611 AN: 152144 Hom.: 3160 Cov.: 32 AF XY: 0.184 AC XY: 13656 AN XY: 74366

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.155

Alfa AF: 0.228 Hom.: 5532

Bravo AF: 0.165

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.086
DANN	Benign	0.72

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: rs1570555; hg19: chr13-76371876;