dbSNP rs11175593: LINC02471:n.1471C>T (chr12-40208138-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.474

Publications

74 publications found

Variant links:

Genes affected

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

LINC02471 links:

LOC105369735 (HGNC:):

LOC105369735 links:

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 links:

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

LRRK2-DT links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105369735	XR_007063560.1 link	n.451C>T	non_coding_transcript_exon_variant	Exon 2 of 2
LRRK2-DT	NR_186756.1 link	n.164+15521G>A	intron_variant	Intron 1 of 6
LRRK2-DT	NR_186757.1 link	n.164+15521G>A	intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
LINC02471	ENST00000641941.1 link	n.1471C>T	non_coding_transcript_exon_variant	Exon 7 of 7
LRRK2	ENST00000416796.5 link	c.-63+11365C>T	intron_variant	Intron 1 of 14	3	ENSP00000398726.1
LRRK2-DT	ENST00000412812.2 link	n.237+15521G>A	intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0299

AC:

4556

AN:

152130

Hom.:

203

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0299

AC:

4558

AN:

152248

Hom.:

204

Cov.:

AF XY:

0.0327

AC XY:

2434

AN XY:

74440

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.0199

AC:

1353

AN:

68016

Other (OTH)

AF:

0.0388

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

214

428

643

857

1071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

(source)

DANN

Benign

0.52

PhyloP100

-0.47

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over