11-22250324-A-T

Position:

chr11-22250324-A-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1

The NM_213599.3(ANO5):c.966A>T(p.Leu322Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 1,612,376 control chromosomes in the GnomAD database, including 247,717 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L322L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.44 ( 17544 hom., cov: 32)

Exomes 𝑓: 0.55 ( 230173 hom. )

Consequence

ANO5
NM_213599.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:18O:1

Conservation

PhyloP100: 0.00100

Variant links:

Genes affected

ANO5 (HGNC:27337): (anoctamin 5) This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]

ANO5 links:

ANO5 (HGNC:):

ANO5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a topological_domain Extracellular (size 59) in uniprot entity ANO5_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_213599.3

BP4

Computational evidence support a benign effect (MetaRNN=2.8172135E-4).

BP6

Variant 11-22250324-A-T is Benign according to our data. Variant chr11-22250324-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 96687.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-22250324-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANO5	NM_213599.3 linkuse as main transcript	c.966A>T	p.Leu322Phe	missense_variant	10/22	ENST00000324559.9	NP_998764.1	Q75V66

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO5	ENST00000324559.9 linkuse as main transcript	c.966A>T	p.Leu322Phe	missense_variant	10/22	1	NM_213599.3	ENSP00000315371.9		Q75V66

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66910

AN:

151890

Hom.:

17535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.559

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.609

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.593

Gnomad OTH

AF:

0.486

GnomAD3 exomes

AF:

0.478

AC:

119591

AN:

250046

Hom.:

31869

AF XY:

0.496

AC XY:

66987

AN XY:

135148

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.298

Gnomad ASJ exome

AF:

0.602

Gnomad EAS exome

AF:

0.179

Gnomad SAS exome

AF:

0.503

Gnomad FIN exome

AF:

0.590

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.525

GnomAD4 exome

AF:

0.550

AC:

803860

AN:

1460368

Hom.:

230173

Cov.:

AF XY:

0.552

AC XY:

400941

AN XY:

726446

show subpopulations

Gnomad4 AFR exome

AF:

0.152

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.611

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.507

Gnomad4 FIN exome

AF:

0.581

Gnomad4 NFE exome

AF:

0.588

Gnomad4 OTH exome

AF:

0.522

GnomAD4 genome

AF:

0.440

AC:

66928

AN:

152008

Hom.:

17544

Cov.:

AF XY:

0.440

AC XY:

32712

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.609

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.501

Gnomad4 FIN

AF:

0.594

Gnomad4 NFE

AF:

0.593

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.549

Hom.:

17185

Bravo

AF:

0.407

TwinsUK

AF:

0.576

AC:

2137

ALSPAC

AF:

0.585

AC:

2254

ESP6500AA

AF:

0.180

AC:

794

ESP6500EA

AF:

0.586

AC:

5041

ExAC

AF:

0.480

AC:

58309

Asia WGS

AF:

0.325

AC:

1136

AN:

3476

EpiCase

AF:

0.581

EpiControl

AF:

0.584

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:18Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:10

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2015	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 15, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 15, 2013	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jan 07, 2016	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 13, 2015	p.Leu322Phe in exon 10 of ANO5: This variant is not expected to have clinical si gnificance because it has been identified in 41.4% (3559/8600) of European Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs7481951). -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 12, 2017	- -

not provided

Benign:1Other:1

not provided, no classification provided	literature only	ANO5 @LOVD	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Miyoshi muscular dystrophy 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Limb-girdle muscular dystrophy, recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

ANO5-Related Muscle Diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Gnathodiaphyseal dysplasia;C1969785:Autosomal recessive limb-girdle muscular dystrophy type 2L

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Gnathodiaphyseal dysplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Autosomal recessive limb-girdle muscular dystrophy type 2L

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Miyoshi myopathy

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.10

Eigen

Benign

-0.54

Eigen_PC

Benign

-0.45

FATHMM_MKL

Benign

0.084

LIST_S2

Benign

0.85

MetaRNN

Benign

0.00028

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.3

PrimateAI

Benign

0.41

PROVEAN

Benign

-2.3

REVEL

Benign

0.054

Sift

Benign

0.14

Sift4G

Uncertain

0.059

Polyphen

0.011

Vest4

0.046

MutPred

0.17

Loss of catalytic residue at L322 (P = 0.1168);

MPC

0.10

ClinPred

0.0038

GERP RS

3.0

Varity_R

0.10

gMVP

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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