chr1-26114549-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_152835.5(PDIK1L):c.241G>A(p.Val81Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,102 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 (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
PDIK1L
NM_152835.5 missense
NM_152835.5 missense
Scores
1
5
10
Clinical Significance
Conservation
PhyloP100: 9.59
Genes affected
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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;
PP2
Missense variant where missense usually causes diseases, PDIK1L
BP4
Computational evidence support a benign effect (MetaRNN=0.096726865).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDIK1L | NM_152835.5 | c.241G>A | p.Val81Met | missense_variant | 2/3 | ENST00000374269.2 | |
PDIK1L | NM_001243532.2 | c.241G>A | p.Val81Met | missense_variant | 2/3 | ||
PDIK1L | NM_001243533.2 | c.241G>A | p.Val81Met | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIK1L | ENST00000374269.2 | c.241G>A | p.Val81Met | missense_variant | 2/3 | 1 | NM_152835.5 | P1 | |
PDIK1L | ENST00000374271.8 | c.241G>A | p.Val81Met | missense_variant | 3/4 | 1 | P1 | ||
PDIK1L | ENST00000619836.4 | c.241G>A | p.Val81Met | missense_variant | 2/3 | 3 | P1 | ||
PDIK1L | ENST00000444713.5 | c.241G>A | p.Val81Met | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251166Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135798
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GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727192
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74464
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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 | Aug 08, 2023 | The c.241G>A (p.V81M) alteration is located in exon 2 (coding exon 1) of the PDIK1L gene. This alteration results from a G to A substitution at nucleotide position 241, causing the valine (V) at amino acid position 81 to be replaced by a methionine (M). 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
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;.;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T;T
Polyphen
B;.;B;B
Vest4
MutPred
Gain of disorder (P = 0.0412);Gain of disorder (P = 0.0412);Gain of disorder (P = 0.0412);Gain of disorder (P = 0.0412);
MVP
MPC
1.1
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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