chr3-197982912-A-G

Variant names:

• chr3-197982912-A-G
• rs6770002
• NM_001136049.3:c.705-1031A>G

Variant summary

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

The NM_001136049.3(LMLN):​c.705-1031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,290 control chromosomes in the GnomAD database, including 378 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 0.065 (378 hom., cov: 32)
• Consequence: LMLN NM_001136049.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMLN	NM_001136049.3	c.705-1031A>G		intron_variant	Intron 6 of 16	ENST00000420910.7	NP_001129521.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMLN	ENST00000420910.7	c.705-1031A>G		intron_variant	Intron 6 of 16	1	NM_001136049.3	ENSP00000410926.3

Frequencies

GnomAD3 genomes AF: 0.0646 AC: 9827 AN: 152172 Hom.: 376 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0646 AC: 9844 AN: 152290 Hom.: 378 Cov.: 32 AF XY: 0.0601 AC XY: 4474 AN XY: 74474

African (AFR) AF: 0.0997 AC: 4141 AN: 41548

American (AMR) AF: 0.0492 AC: 753 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5180

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4824

European-Finnish (FIN) AF: 0.0152 AC: 161 AN: 10622

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4029 AN: 68030

Other (OTH) AF: 0.0775 AC: 164 AN: 2116

Alfa AF: 0.0599 Hom.: 43

Bravo AF: 0.0684

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.86
PhyloP100		-1.3
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: rs6770002; hg19: chr3-197709783;