ENST00000641941.1:n.1471C>T

Variant names:

• chr12-40208138-C-T
• rs11175593
• ENST00000641941.1:n.1471C>T

Variant summary

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

The ENST00000641941.1(LINC02471):​n.1471C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0299 in 152,248 control chromosomes in the GnomAD database, including 204 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 0.030 (204 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02471 ENST00000641941.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 74 publications found

Genes affected

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

LOC105369735 (HGNC:):

LRRK2 (HGNC:18618): (leucine rich repeat kinase 2) This gene is a member of the leucine-rich repeat kinase family and encodes a protein with an ankryin repeat region, a leucine-rich repeat (LRR) domain, a kinase domain, a DFG-like motif, a RAS domain, a GTPase domain, a MLK-like domain, and a WD40 domain. The protein is present largely in the cytoplasm but also associates with the mitochondrial outer membrane. Mutations in this gene have been associated with Parkinson disease-8. [provided by RefSeq, Jul 2008]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641941.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRK2-DT	NR_186756.1		n.164+15521G>A		intron	N/A
	LRRK2-DT	NR_186757.1		n.164+15521G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02471	ENST00000641941.1		n.1471C>T		non_coding_transcript_exon	Exon 7 of 7
	LRRK2	ENST00000416796.5	TSL:3	c.-63+11365C>T		intron	N/A	ENSP00000398726.1
	LRRK2-DT	ENST00000412812.2	TSL:4	n.237+15521G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0299 AC: 4556 AN: 152130 Hom.: 203 Cov.: 33

Gnomad AFR AF: 0.00662

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0397

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0299 AC: 4558 AN: 152248 Hom.: 204 Cov.: 33 AF XY: 0.0327 AC XY: 2434 AN XY: 74440

African (AFR) AF: 0.00660 AC: 274 AN: 41538

American (AMR) AF: 0.112 AC: 1707 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3472

East Asian (EAS) AF: 0.0456 AC: 237 AN: 5192

South Asian (SAS) AF: 0.0640 AC: 309 AN: 4830

European-Finnish (FIN) AF: 0.0288 AC: 305 AN: 10588

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0199 AC: 1353 AN: 68016

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0285 Hom.: 614

Bravo AF: 0.0372

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs11175593; hg19: chr12-40601940;