Variant 2-241188699-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The ENST00000274979.12(ANO7):c.88C>T(p.Arg30Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00378 in 1,613,612 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 44 hom. )

Consequence

ANO7
ENST00000274979.12 stop_gained

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.98

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Stoplost variant in ENST00000274979.12 Downstream stopcodon found after 967 codons.

BP6

Variant 2-241188699-C-T is Benign according to our data. Variant chr2-241188699-C-T is described in ClinVar as [Benign]. Clinvar id is 715796.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO7	NM_001370694.2 linkuse as main transcript	c.-75C>T		5_prime_UTR_variant	1/25	ENST00000674324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO7	ENST00000274979.12 linkuse as main transcript	c.88C>T	p.Arg30Ter	stop_gained	1/25	1		P2	Q6IWH7-1
ANO7	ENST00000674324.2 linkuse as main transcript	c.-75C>T		5_prime_UTR_variant	1/25		NM_001370694.2	A2
ANO7	ENST00000402530.8 linkuse as main transcript	c.-75C>T		5_prime_UTR_variant	1/4	1
ANO7	ENST00000402430.8 linkuse as main transcript	c.-75C>T		5_prime_UTR_variant	1/22	5

Frequencies

GnomAD3 genomes

AF:

0.00414

AC:

630

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000482

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000523

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0342

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00344

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00555

AC:

1380

AN:

248768

Hom.:

AF XY:

0.00512

AC XY:

690

AN XY:

134838

show subpopulations

Gnomad AFR exome

AF:

0.000371

Gnomad AMR exome

AF:

0.000261

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0354

Gnomad NFE exome

AF:

0.00504

Gnomad OTH exome

AF:

0.00639

GnomAD4 exome

AF:

0.00374

AC:

5466

AN:

1461302

Hom.:

Cov.:

AF XY:

0.00356

AC XY:

2589

AN XY:

726996

show subpopulations

Gnomad4 AFR exome

AF:

0.000358

Gnomad4 AMR exome

AF:

0.000380

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0345

Gnomad4 NFE exome

AF:

0.00310

Gnomad4 OTH exome

AF:

0.00272

GnomAD4 genome

AF:

0.00414

AC:

630

AN:

152310

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

385

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000481

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0342

Gnomad4 NFE

AF:

0.00344

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00274

Hom.:

Bravo

AF:

0.00164

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00314

AC:

ExAC

AF:

0.00568

AC:

690

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00234

EpiControl

AF:

0.00225

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

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

Cadd

Benign

Dann

Benign

0.97

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.99

FATHMM_MKL

Benign

0.025

MutationTaster

Benign

1.0

A;A;A

Vest4

0.10

GERP RS

-2.1

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.

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