ENST00000412812.2:n.503-455C>T

Variant names:

• chr12-40186638-G-A
• rs2046932
• ENST00000412812.2:n.503-455C>T

Variant summary

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

The ENST00000412812.2(LRRK2-DT):​n.503-455C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 152,212 control chromosomes in the GnomAD database, including 270 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 0.050 (270 hom., cov: 32)
• Consequence: LRRK2-DT ENST00000412812.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 12 publications found

Genes affected

LRRK2-DT (HGNC:40848): (LRRK2 divergent transcript)

LINC02471 (HGNC:53410): (long intergenic non-protein coding RNA 2471)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412812.2. 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
	LRRK2-DT	NR_186756.1		n.430-1017C>T		intron	N/A
	LRRK2-DT	NR_186757.1		n.165-19271C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRK2-DT	ENST00000412812.2	TSL:4	n.503-455C>T		intron	N/A
	LINC02471	ENST00000641941.1		n.232-11568G>A		intron	N/A
	LINC02471	ENST00000783096.1		n.156-16814G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7610 AN: 152094 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0311

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0500 AC: 7613 AN: 152212 Hom.: 270 Cov.: 32 AF XY: 0.0493 AC XY: 3666 AN XY: 74428

African (AFR) AF: 0.0144 AC: 600 AN: 41536

American (AMR) AF: 0.0377 AC: 576 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5184

South Asian (SAS) AF: 0.136 AC: 654 AN: 4820

European-Finnish (FIN) AF: 0.0311 AC: 329 AN: 10586

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0694 AC: 4718 AN: 68010

Other (OTH) AF: 0.0573 AC: 121 AN: 2112

Alfa AF: 0.0593 Hom.: 207

Bravo AF: 0.0474

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.4
DANN	Benign	0.83
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2046932; hg19: chr12-40580440;