rs11175593
Positions:
Variant summary
Our verdict is Benign. Variant got -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
ENST00000641941.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.474
Genes affected
LINC02471 (HGNC:53410): (long intergenic non-protein coding RNA 2471)
LRRK2-DT (HGNC:40848): (LRRK2 divergent transcript)
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -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 | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105369735 | XR_007063561.1 | n.420+141C>T | intron_variant, non_coding_transcript_variant | ||||
LOC105369735 | XR_007063560.1 | n.451C>T | non_coding_transcript_exon_variant | 2/2 | |||
LOC105369735 | XR_944865.4 | n.310+141C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02471 | ENST00000641941.1 | n.1471C>T | non_coding_transcript_exon_variant | 7/7 | |||||
LRRK2-DT | ENST00000412812.1 | n.145+15521G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
LRRK2 | ENST00000416796.5 | c.-63+11365C>T | intron_variant | 3 | |||||
LINC02471 | ENST00000661406.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0299 AC: 4556AN: 152130Hom.: 203 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
4556
AN:
152130
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
2
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
2
Gnomad4 AFR exome
AF:
GnomAD4 genome ? AF: 0.0299 AC: 4558AN: 152248Hom.: 204 Cov.: 33 AF XY: 0.0327 AC XY: 2434AN XY: 74440
GnomAD4 genome
?
AF:
AC:
4558
AN:
152248
Hom.:
Cov.:
33
AF XY:
AC XY:
2434
AN XY:
74440
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
186
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at