rs9530460

Variant names:

• chr13-75684934-T-C
• rs9530460
• NM_001306080.2:c.70-28248T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306080.2(LMO7):​c.70-28248T>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
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	NM_001306080.2	MANE Select	c.70-28248T>C		intron	N/A	NP_001293009.1	F8WD26
	LMO7	NM_005358.5		c.226-28248T>C		intron	N/A	NP_005349.3	Q8WWI1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMO7	ENST00000377534.8	TSL:1 MANE Select	c.70-28248T>C		intron	N/A	ENSP00000366757.4	F8WD26
	LMO7	ENST00000341547.8	TSL:1	c.226-28248T>C		intron	N/A	ENSP00000342112.4	Q8WWI1-3
	LMO7	ENST00000357063.7	TSL:5	c.181-28248T>C		intron	N/A	ENSP00000349571.4	J3KP06

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

African (AFR) AF: 0.314 AC: 13027 AN: 41480

American (AMR) AF: 0.359 AC: 5480 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3472

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5188

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4820

European-Finnish (FIN) AF: 0.443 AC: 4683 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34024 AN: 67974

Other (OTH) AF: 0.445 AC: 939 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.48
PhyloP100		0.29
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: rs9530460; hg19: chr13-76259070;