4-20713526-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001258345.3(PACRGL):ā€‹c.596A>Gā€‹(p.His199Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000137 in 1,458,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.000014 ( 0 hom. )

Consequence

PACRGL
NM_001258345.3 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.92
Variant links:
Genes affected
PACRGL (HGNC:28442): (parkin coregulated like)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26513025).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PACRGLNM_001258345.3 linkuse as main transcriptc.596A>G p.His199Arg missense_variant 7/9 ENST00000503585.6 NP_001245274.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PACRGLENST00000503585.6 linkuse as main transcriptc.596A>G p.His199Arg missense_variant 7/92 NM_001258345.3 ENSP00000423881 P1Q8N7B6-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.0000137
AC:
20
AN:
1458404
Hom.:
0
Cov.:
30
AF XY:
0.0000165
AC XY:
12
AN XY:
725742
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
EpiCase
AF:
0.0000546
EpiControl
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 02, 2021The c.596A>G (p.H199R) alteration is located in exon 7 (coding exon 6) of the PACRGL gene. This alteration results from a A to G substitution at nucleotide position 596, causing the histidine (H) at amino acid position 199 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Uncertain
0.015
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
19
DANN
Benign
0.86
DEOGEN2
Benign
0.043
T;.;.;.;.;.;.;.;T;T
Eigen
Benign
0.084
Eigen_PC
Benign
0.18
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.91
D;.;.;T;D;D;T;.;D;D
M_CAP
Benign
0.025
T
MetaRNN
Benign
0.27
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.75
T
MutationAssessor
Uncertain
2.0
M;M;M;.;.;.;.;M;.;.
MutationTaster
Benign
0.84
D;D;N;N;N;N;N;N;N
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-1.4
N;N;N;D;N;N;D;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.65
T;T;T;D;T;T;D;T;T;T
Sift4G
Benign
0.58
T;T;T;T;T;T;T;T;T;T
Polyphen
0.074
B;B;B;.;.;.;.;B;P;.
Vest4
0.66
MutPred
0.47
Gain of MoRF binding (P = 0.0115);Gain of MoRF binding (P = 0.0115);Gain of MoRF binding (P = 0.0115);.;.;Gain of MoRF binding (P = 0.0115);.;Gain of MoRF binding (P = 0.0115);.;.;
MVP
0.24
MPC
0.11
ClinPred
0.44
T
GERP RS
4.4
Varity_R
0.059
gMVP
0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-20715149; API