2-241191524-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001370694.2(ANO7):​c.166+273T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,100 control chromosomes in the GnomAD database, including 8,267 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 8267 hom., cov: 32)

Consequence

ANO7
NM_001370694.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.284
Variant links:
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=-0.83).
BP6
Variant 2-241191524-T-A is Benign according to our data. Variant chr2-241191524-T-A is described in ClinVar as [Benign]. Clinvar id is 1267835.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANO7NM_001370694.2 linkuse as main transcriptc.166+273T>A intron_variant ENST00000674324.2 NP_001357623.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANO7ENST00000674324.2 linkuse as main transcriptc.166+273T>A intron_variant NM_001370694.2 ENSP00000501393 A2
ANO7ENST00000274979.12 linkuse as main transcriptc.328+273T>A intron_variant 1 ENSP00000274979 P2Q6IWH7-1
ANO7ENST00000402530.8 linkuse as main transcriptc.166+273T>A intron_variant 1 ENSP00000383985
ANO7ENST00000402430.8 linkuse as main transcriptc.166+273T>A intron_variant 5 ENSP00000385418

Frequencies

GnomAD3 genomes
AF:
0.292
AC:
44412
AN:
151982
Hom.:
8271
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0850
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.277
Gnomad ASJ
AF:
0.450
Gnomad EAS
AF:
0.0686
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.414
Gnomad OTH
AF:
0.334
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.292
AC:
44399
AN:
152100
Hom.:
8267
Cov.:
32
AF XY:
0.289
AC XY:
21487
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0846
Gnomad4 AMR
AF:
0.277
Gnomad4 ASJ
AF:
0.450
Gnomad4 EAS
AF:
0.0690
Gnomad4 SAS
AF:
0.227
Gnomad4 FIN
AF:
0.399
Gnomad4 NFE
AF:
0.414
Gnomad4 OTH
AF:
0.331
Alfa
AF:
0.351
Hom.:
1296
Bravo
AF:
0.278
Asia WGS
AF:
0.156
AC:
546
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 submitterclinical testingGeneDxNov 11, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.8
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2074837; hg19: chr2-242130939; API