2-241190100-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001370694.2(ANO7):c.37G>A(p.Val13Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,584,012 control chromosomes in the GnomAD database, including 7,769 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.051 ( 977 hom., cov: 32)
Exomes 𝑓: 0.031 ( 6792 hom. )
Consequence
ANO7
NM_001370694.2 missense
NM_001370694.2 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -0.178
Genes affected
ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=2.9236078E-4).
BP6
?
Variant 2-241190100-G-A is Benign according to our data. Variant chr2-241190100-G-A is described in ClinVar as [Benign]. Clinvar id is 1246662.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO7 | NM_001370694.2 | c.37G>A | p.Val13Ile | missense_variant | 2/25 | ENST00000674324.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO7 | ENST00000674324.2 | c.37G>A | p.Val13Ile | missense_variant | 2/25 | NM_001370694.2 | A2 | ||
ANO7 | ENST00000274979.12 | c.199G>A | p.Val67Ile | missense_variant | 2/25 | 1 | P2 | ||
ANO7 | ENST00000402530.8 | c.37G>A | p.Val13Ile | missense_variant | 2/4 | 1 | |||
ANO7 | ENST00000402430.8 | c.37G>A | p.Val13Ile | missense_variant | 2/22 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0507 AC: 7704AN: 152070Hom.: 973 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0947 AC: 19169AN: 202344Hom.: 3177 AF XY: 0.0848 AC XY: 9219AN XY: 108726
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GnomAD4 exome AF: 0.0308 AC: 44055AN: 1431824Hom.: 6792 Cov.: 32 AF XY: 0.0310 AC XY: 21969AN XY: 709384
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GnomAD4 genome ? AF: 0.0507 AC: 7713AN: 152188Hom.: 977 Cov.: 32 AF XY: 0.0587 AC XY: 4366AN XY: 74396
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ESP6500AA
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ExAC
?
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8519
Asia WGS
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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 | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;B;.
Vest4
MPC
0.087
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