rs9530460

Positions:

• chr13-75684934-T-C
• chr13-75684934-T-G

Variant summary

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

The NM_001306080.2(LMO7):​c.70-28248T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,076 control chromosomes in the GnomAD database, including 13,958 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 0.41 (13958 hom., cov: 32)
• Consequence: LMO7 NM_001306080.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO7	NM_001306080.2	c.70-28248T>C		intron_variant		ENST00000377534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO7	ENST00000377534.8	c.70-28248T>C		intron_variant		1	NM_001306080.2	P2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62246 AN: 151958 Hom.: 13942 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.410 AC: 62301 AN: 152076 Hom.: 13958 Cov.: 32 AF XY: 0.403 AC XY: 29968 AN XY: 74360

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.445

Alfa AF: 0.338 Hom.: 1350

Bravo AF: 0.398

Asia WGS AF: 0.227 AC: 793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.48

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: rs9530460; hg19: chr13-76259070;