Variant chr2-241190072-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001370694.2(ANO7):c.9G>T(p.Arg3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,574,504 control chromosomes in the GnomAD database, including 56,240 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4137 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52103 hom. )

Consequence

ANO7
NM_001370694.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.145

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]

ANO7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 2-241190072-G-T is Benign according to our data. Variant chr2-241190072-G-T is described in ClinVar as [Benign]. Clinvar id is 1182026.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.145 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2 linkuse as main transcript	c.9G>T	p.Arg3=	synonymous_variant	2/25	ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000674324.2 linkuse as main transcript	c.9G>T	p.Arg3=	synonymous_variant	2/25		NM_001370694.2	A2
ANO7	ENST00000274979.12 linkuse as main transcript	c.171G>T	p.Arg57=	synonymous_variant	2/25	1		P2	Q6IWH7-1
ANO7	ENST00000402530.8 linkuse as main transcript	c.9G>T	p.Arg3=	synonymous_variant	2/4	1
ANO7	ENST00000402430.8 linkuse as main transcript	c.9G>T	p.Arg3=	synonymous_variant	2/22	5

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33339

AN:

152006

Hom.:

4135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.0239

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.215

AC:

40907

AN:

189942

Hom.:

5062

AF XY:

0.216

AC XY:

21929

AN XY:

101578

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.174

Gnomad ASJ exome

AF:

0.216

Gnomad EAS exome

AF:

0.0215

Gnomad SAS exome

AF:

0.167

Gnomad FIN exome

AF:

0.291

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.263

AC:

374685

AN:

1422380

Hom.:

52103

Cov.:

AF XY:

0.260

AC XY:

183164

AN XY:

703762

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.0166

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.293

Gnomad4 NFE exome

AF:

0.288

Gnomad4 OTH exome

AF:

0.241

GnomAD4 genome

AF:

0.219

AC:

33347

AN:

152124

Hom.:

4137

Cov.:

AF XY:

0.217

AC XY:

16171

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.0237

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.256

Hom.:

2694

Bravo

AF:

0.207

Asia WGS

AF:

0.104

AC:

361

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over