rs7997101

Variant names:

• chr13-75760682-C-A
• rs7997101
• ENST00000465261.6:c.-739C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-75760682-C-A
• chr13-75760682-C-G
• chr13-75760682-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015842.2(LMO7):​c.-739C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LMO7 NM_015842.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 15 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015842.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	NM_001306080.2	MANE Select	c.211-250C>A		intron	N/A	NP_001293009.1	F8WD26
	LMO7	NM_015842.2		c.-739C>A		5_prime_UTR	Exon 1 of 27	NP_056667.2	Q8WWI1
	LMO7	NM_001366633.2		c.85-250C>A		intron	N/A	NP_001353562.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	ENST00000465261.6	TSL:1	c.-739C>A		5_prime_UTR	Exon 1 of 27	ENSP00000433352.1	A0A0A0MTE2
	LMO7	ENST00000377534.8	TSL:1 MANE Select	c.211-250C>A		intron	N/A	ENSP00000366757.4	F8WD26
	LMO7	ENST00000341547.8	TSL:1	c.367-250C>A		intron	N/A	ENSP00000342112.4	Q8WWI1-3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		0.61
PromoterAI		0.015	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7997101; hg19: chr13-76334818;