chr12-5635329-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001364791.2(ANO2):c.1639A>G(p.Ile547Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,580,150 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0069 ( 56 hom. )
Consequence
ANO2
NM_001364791.2 missense
NM_001364791.2 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: 0.838
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006821841).
BP6
?
Variant 12-5635329-T-C is Benign according to our data. Variant chr12-5635329-T-C is described in ClinVar as [Benign]. Clinvar id is 770983.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO2 | NM_001364791.2 | c.1639A>G | p.Ile547Val | missense_variant | 16/25 | ENST00000682330.1 | |
ANO2 | NM_001278596.3 | c.1654A>G | p.Ile552Val | missense_variant | 18/27 | ||
ANO2 | NM_001278597.3 | c.1642A>G | p.Ile548Val | missense_variant | 18/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO2 | ENST00000682330.1 | c.1639A>G | p.Ile547Val | missense_variant | 16/25 | NM_001364791.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00636 AC: 967AN: 152090Hom.: 10 Cov.: 32
GnomAD3 genomes
?
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967
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32
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GnomAD3 exomes AF: 0.00750 AC: 1602AN: 213594Hom.: 12 AF XY: 0.00727 AC XY: 843AN XY: 116014
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GnomAD4 exome AF: 0.00694 AC: 9916AN: 1427942Hom.: 56 Cov.: 31 AF XY: 0.00673 AC XY: 4774AN XY: 708978
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GnomAD4 genome ? AF: 0.00635 AC: 967AN: 152208Hom.: 10 Cov.: 32 AF XY: 0.00708 AC XY: 527AN XY: 74426
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ESP6500AA
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ExAC
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1027
Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 02, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;.;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
REVEL
Benign
Sift4G
Benign
T;T;T;.
Vest4
MVP
MPC
0.061
ClinPred
T
GERP RS
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