3-197980051-G-A

Position:

• chr3-197980051-G-A

Variant summary

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

The NM_001136049.3(LMLN):​c.526-275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,924 control chromosomes in the GnomAD database, including 14,818 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 0.37 (14818 hom., cov: 32)
• Consequence: LMLN NM_001136049.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

LMLN (HGNC:15991): (leishmanolysin like peptidase) This gene encodes a zinc-metallopeptidase. The encoded protein may play a role in cell migration and invasion. Studies of a similar protein in Drosophila indicate a potential role in mitotic progression. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMLN	NM_001136049.3	c.526-275G>A		intron_variant		ENST00000420910.7	NP_001129521.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMLN	ENST00000420910.7	c.526-275G>A		intron_variant		1	NM_001136049.3	ENSP00000410926

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56439 AN: 151806 Hom.: 14760 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.372 AC: 56559 AN: 151924 Hom.: 14818 Cov.: 32 AF XY: 0.365 AC XY: 27092 AN XY: 74226

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.321

Alfa AF: 0.254 Hom.: 5615

Bravo AF: 0.383

Asia WGS AF: 0.242 AC: 844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.27

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: rs7374380; hg19: chr3-197706922;