chr2-241195442-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001370694.2(ANO7):c.167-261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,160 control chromosomes in the GnomAD database, including 51,891 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.83 ( 51891 hom., cov: 32)
Consequence
ANO7
NM_001370694.2 intron
NM_001370694.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.357
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 2-241195442-A-G is Benign according to our data. Variant chr2-241195442-A-G is described in ClinVar as [Benign]. Clinvar id is 1229920.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO7 | NM_001370694.2 | c.167-261A>G | intron_variant | ENST00000674324.2 | NP_001357623.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANO7 | ENST00000674324.2 | c.167-261A>G | intron_variant | NM_001370694.2 | ENSP00000501393 | A2 | ||||
ANO7 | ENST00000274979.12 | c.329-261A>G | intron_variant | 1 | ENSP00000274979 | P2 | ||||
ANO7 | ENST00000402530.8 | c.167-264A>G | intron_variant | 1 | ENSP00000383985 | |||||
ANO7 | ENST00000402430.8 | c.167-264A>G | intron_variant | 5 | ENSP00000385418 |
Frequencies
GnomAD3 genomes AF: 0.825 AC: 125463AN: 152042Hom.: 51839 Cov.: 32
GnomAD3 genomes
AF:
AC:
125463
AN:
152042
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.825 AC: 125568AN: 152160Hom.: 51891 Cov.: 32 AF XY: 0.828 AC XY: 61554AN XY: 74382
GnomAD4 genome
AF:
AC:
125568
AN:
152160
Hom.:
Cov.:
32
AF XY:
AC XY:
61554
AN XY:
74382
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2953
AN:
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 | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at