8-100522584-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001270377.2(ANKRD46):c.658G>A(p.Val220Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000861 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000092 ( 0 hom. )
Consequence
ANKRD46
NM_001270377.2 missense
NM_001270377.2 missense
Scores
1
2
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.12
Genes affected
ANKRD46 (HGNC:27229): (ankyrin repeat domain 46) This gene encodes a protein containing multiple ankyrin repeats. Ankyrin domains function in protein-protein interactions in a variety of cellular processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]
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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=0.22038764).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD46 | NM_001270377.2 | c.658G>A | p.Val220Met | missense_variant | 5/5 | ENST00000335659.7 | |
ANKRD46 | NM_001270378.2 | c.658G>A | p.Val220Met | missense_variant | 5/5 | ||
ANKRD46 | NM_198401.4 | c.658G>A | p.Val220Met | missense_variant | 6/6 | ||
ANKRD46 | NM_001270379.2 | c.636+22G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD46 | ENST00000335659.7 | c.658G>A | p.Val220Met | missense_variant | 5/5 | 1 | NM_001270377.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251320Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135828
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GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461862Hom.: 0 Cov.: 34 AF XY: 0.0000990 AC XY: 72AN XY: 727230
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74298
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
P;P;P;.
Vest4
MVP
ClinPred
T
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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