2-241189032-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.-8+266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,142 control chromosomes in the GnomAD database, including 10,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 10663 hom., cov: 33)

Consequence

ANO7
NM_001370694.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.215
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=-0.9).
BP6
Variant 2-241189032-G-A is Benign according to our data. Variant chr2-241189032-G-A is described in ClinVar as [Benign]. Clinvar id is 1247216.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANO7NM_001370694.2 linkuse as main transcriptc.-8+266G>A intron_variant ENST00000674324.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANO7ENST00000674324.2 linkuse as main transcriptc.-8+266G>A intron_variant NM_001370694.2 A2
ANO7ENST00000274979.12 linkuse as main transcriptc.155+266G>A intron_variant 1 P2Q6IWH7-1
ANO7ENST00000402530.8 linkuse as main transcriptc.-8+266G>A intron_variant 1
ANO7ENST00000402430.8 linkuse as main transcriptc.-8+266G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.350
AC:
53133
AN:
152024
Hom.:
10671
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.508
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.110
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.388
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.457
Gnomad OTH
AF:
0.387
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.349
AC:
53116
AN:
152142
Hom.:
10663
Cov.:
33
AF XY:
0.344
AC XY:
25565
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.184
Gnomad4 AMR
AF:
0.307
Gnomad4 ASJ
AF:
0.541
Gnomad4 EAS
AF:
0.110
Gnomad4 SAS
AF:
0.363
Gnomad4 FIN
AF:
0.388
Gnomad4 NFE
AF:
0.457
Gnomad4 OTH
AF:
0.383
Alfa
AF:
0.387
Hom.:
1487
Bravo
AF:
0.340
Asia WGS
AF:
0.241
AC:
842
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 testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.0
DANN
Benign
0.61

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: rs11694282; hg19: chr2-242128447; API