chr11-35435978-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001001991.3(PAMR1):c.1258C>T(p.Arg420Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
PAMR1
NM_001001991.3 missense
NM_001001991.3 missense
Scores
4
5
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 10.0
Genes affected
PAMR1 (HGNC:24554): (peptidase domain containing associated with muscle regeneration 1) Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAMR1 | NM_001001991.3 | c.1258C>T | p.Arg420Cys | missense_variant | 9/11 | ENST00000619888.5 | |
PAMR1 | NM_015430.4 | c.1309C>T | p.Arg437Cys | missense_variant | 10/12 | ||
PAMR1 | NM_001282675.2 | c.1138C>T | p.Arg380Cys | missense_variant | 11/13 | ||
PAMR1 | NM_001282676.2 | c.925C>T | p.Arg309Cys | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAMR1 | ENST00000619888.5 | c.1258C>T | p.Arg420Cys | missense_variant | 9/11 | 1 | NM_001001991.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251448Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135896
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GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727248
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
Sift4G
Uncertain
D;D;D;D;D;D
Polyphen
D;D;.;.;.;.
Vest4
MutPred
0.53
.;Loss of MoRF binding (P = 0.0099);.;.;.;.;
MVP
ClinPred
D
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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