Variant 2-241190100-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.178

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 -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
ANO7	NM_001370694.2 linkuse as main transcript	c.37G>A	p.Val13Ile	missense_variant	2/25	ENST00000674324.2	NP_001357623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO7	ENST00000674324.2 linkuse as main transcript	c.37G>A	p.Val13Ile	missense_variant	2/25		NM_001370694.2	ENSP00000501393	A2
ANO7	ENST00000274979.12 linkuse as main transcript	c.199G>A	p.Val67Ile	missense_variant	2/25	1		ENSP00000274979	P2	Q6IWH7-1
ANO7	ENST00000402530.8 linkuse as main transcript	c.37G>A	p.Val13Ile	missense_variant	2/4	1		ENSP00000383985
ANO7	ENST00000402430.8 linkuse as main transcript	c.37G>A	p.Val13Ile	missense_variant	2/22	5		ENSP00000385418

Frequencies

GnomAD3 genomes

AF:

0.0507

AC:

7704

AN:

152070

Hom.:

973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0271

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.0945

Gnomad FIN

AF:

0.0339

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00462

Gnomad OTH

AF:

0.0632

GnomAD3 exomes

AF:

0.0947

AC:

19169

AN:

202344

Hom.:

3177

AF XY:

0.0848

AC XY:

9219

AN XY:

108726

show subpopulations

Gnomad AFR exome

AF:

0.0268

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.00322

Gnomad EAS exome

AF:

0.454

Gnomad SAS exome

AF:

0.0765

Gnomad FIN exome

AF:

0.0365

Gnomad NFE exome

AF:

0.00459

Gnomad OTH exome

AF:

0.0676

GnomAD4 exome

AF:

0.0308

AC:

44055

AN:

1431824

Hom.:

6792

Cov.:

AF XY:

0.0310

AC XY:

21969

AN XY:

709384

show subpopulations

Gnomad4 AFR exome

AF:

0.0235

Gnomad4 AMR exome

AF:

0.290

Gnomad4 ASJ exome

AF:

0.00184

Gnomad4 EAS exome

AF:

0.471

Gnomad4 SAS exome

AF:

0.0769

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.00261

Gnomad4 OTH exome

AF:

0.0458

GnomAD4 genome

AF:

0.0507

AC:

7713

AN:

152188

Hom.:

977

Cov.:

AF XY:

0.0587

AC XY:

4366

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0270

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.0948

Gnomad4 FIN

AF:

0.0339

Gnomad4 NFE

AF:

0.00462

Gnomad4 OTH

AF:

0.0626

Alfa

AF:

0.0167

Hom.:

362

Bravo

AF:

0.0647

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.0266

AC:

117

ESP6500EA

AF:

0.00385

AC:

ExAC

AF:

0.0711

AC:

8519

Asia WGS

AF:

0.226

AC:

784

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.029

.;T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.059

LIST_S2

Benign

0.50

T;T;T

MetaRNN

Benign

0.00029

T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.0

N;N;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.36

PROVEAN

Benign

-0.43

N;N;N

REVEL

Benign

0.036

Sift

Benign

0.15

T;T;T

Sift4G

Benign

0.11

T;T;T

Polyphen

0.71

P;B;.

Vest4

0.073

MPC

0.087

ClinPred

0.0011

GERP RS

0.53

Varity_R

0.030

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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