chr4-20704716-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001258345.3(PACRGL):c.109C>A(p.Gln37Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
PACRGL
NM_001258345.3 missense
NM_001258345.3 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 3.67
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13067129).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PACRGL | NM_001258345.3 | c.109C>A | p.Gln37Lys | missense_variant | 3/9 | ENST00000503585.6 | NP_001245274.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PACRGL | ENST00000503585.6 | c.109C>A | p.Gln37Lys | missense_variant | 3/9 | 2 | NM_001258345.3 | ENSP00000423881 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 34
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34
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
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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 submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.109C>A (p.Q37K) alteration is located in exon 3 (coding exon 2) of the PACRGL gene. This alteration results from a C to A substitution at nucleotide position 109, causing the glutamine (Q) at amino acid position 37 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;.;.;T;T;.;.;T;.;.;.;.;.;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;.;D;D;D;D;D;D;D;D;D;D;D;D;.;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M;M;.;M;.;.;.;.;.;M;.;.;.;.;M;.;.
MutationTaster
Benign
N;N;N;N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;D;N;N;N;N;D;D;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;D;T;T;T;D;T;D;T;T;D;D;T;T;T
Sift4G
Benign
T;T;T;T;T;D;T;T;T;D;T;T;T;T;D;D;T;T;T
Polyphen
P;B;B;B;.;.;.;.;.;.;.;.;.;.;.;.;B;B;.
Vest4
0.32, 0.34, 0.38, 0.45, 0.29, 0.41
MutPred
0.19
.;Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);Gain of methylation at Q37 (P = 0.0074);
MVP
MPC
0.20
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at