13-75760682-C-T

Position:

• chr13-75760682-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000465261.6(LMO7):​c.-739C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,516,842 control chromosomes in the GnomAD database, including 175,108 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 0.50 (19603 hom., cov: 31)
  • Exomes 𝑓: 0.47 (155505 hom.)
• Consequence: LMO7 ENST00000465261.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMO7	NM_001306080.2	c.211-250C>T		intron_variant		ENST00000377534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMO7	ENST00000377534.8	c.211-250C>T		intron_variant		1	NM_001306080.2	P2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75943 AN: 151694 Hom.: 19602 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.470 AC: 641562 AN: 1365032 Hom.: 155505 Cov.: 34 AF XY: 0.467 AC XY: 313298 AN XY: 671480

Gnomad4 AFR exome AF: 0.520

Gnomad4 AMR exome AF: 0.643

Gnomad4 ASJ exome AF: 0.380

Gnomad4 EAS exome AF: 0.866

Gnomad4 SAS exome AF: 0.411

Gnomad4 FIN exome AF: 0.544

Gnomad4 NFE exome AF: 0.455

Gnomad4 OTH exome AF: 0.468

GnomAD4 genome AF: 0.501 AC: 75988 AN: 151810 Hom.: 19603 Cov.: 31 AF XY: 0.506 AC XY: 37530 AN XY: 74172

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.482

Alfa AF: 0.462 Hom.: 15881

Bravo AF: 0.505

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.92

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: rs7997101; hg19: chr13-76334818;