chr6-163215216-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080379.2(PACRG):​c.614-99611T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,074 control chromosomes in the GnomAD database, including 44,089 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 0.75 ( 44089 hom., cov: 32)

Consequence

PACRG
NM_001080379.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.240
Variant links:
Genes affected
PACRG (HGNC:19152): (parkin coregulated) This gene encodes a protein that is conserved across metazoans. In vertebrates, this gene is linked in a head-to-head arrangement with the adjacent parkin gene, which is associated with autosomal recessive juvenile Parkinson's disease. These genes are co-regulated in various tissues and they share a bi-directional promoter. Both genes are associated with susceptibility to leprosy. The parkin co-regulated gene protein forms a large molecular complex with chaperones, including heat shock proteins 70 and 90, and chaperonin components. This protein is also a component of Lewy bodies in Parkinson's disease patients, and it suppresses unfolded Pael receptor-induced neuronal cell death. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PACRGNM_001080379.2 linkuse as main transcriptc.614-99611T>A intron_variant ENST00000366888.7 NP_001073848.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PACRGENST00000366888.7 linkuse as main transcriptc.614-99611T>A intron_variant 1 NM_001080379.2 ENSP00000355854 P1Q96M98-2

Frequencies

GnomAD3 genomes
AF:
0.754
AC:
114632
AN:
151956
Hom.:
44049
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.904
Gnomad AMI
AF:
0.769
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.700
Gnomad EAS
AF:
0.798
Gnomad SAS
AF:
0.794
Gnomad FIN
AF:
0.666
Gnomad MID
AF:
0.744
Gnomad NFE
AF:
0.677
Gnomad OTH
AF:
0.722
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.754
AC:
114730
AN:
152074
Hom.:
44089
Cov.:
32
AF XY:
0.753
AC XY:
55983
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.904
Gnomad4 AMR
AF:
0.741
Gnomad4 ASJ
AF:
0.700
Gnomad4 EAS
AF:
0.797
Gnomad4 SAS
AF:
0.793
Gnomad4 FIN
AF:
0.666
Gnomad4 NFE
AF:
0.677
Gnomad4 OTH
AF:
0.723
Alfa
AF:
0.713
Hom.:
4853
Bravo
AF:
0.763
Asia WGS
AF:
0.788
AC:
2724
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.71
DANN
Benign
0.53

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2206256; hg19: chr6-163636248; API