dbSNP rs2276068: ANO1:c.1780+16C>G (chr11-70161378-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018043.7(ANO1):c.1780+16C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,611,890 control chromosomes in the GnomAD database, including 223,894 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 18620 hom., cov: 33)

Exomes 𝑓: 0.53 ( 205274 hom. )

Consequence

ANO1
NM_018043.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.238

Publications

7 publications found

Variant links:

Genes affected

ANO1 (HGNC:21625): (anoctamin 1) Enables calcium activated cation channel activity; intracellular calcium activated chloride channel activity; and iodide transmembrane transporter activity. Involved in cation transport; inorganic anion transport; and positive regulation of insulin secretion involved in cellular response to glucose stimulus. Located in apical plasma membrane and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ANO1 Gene-Disease associations (from GenCC):

moyamoya disease 7
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
intestinal dysmotility syndrome
Inheritance: AR Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ANO1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO1	NM_018043.7 link	c.1780+16C>G		intron_variant	Intron 17 of 25	ENST00000355303.10	NP_060513.5	Q5XXA6-1Q9NW72

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO1	ENST00000355303.10 link	c.1780+16C>G		intron_variant	Intron 17 of 25	1	NM_018043.7	ENSP00000347454.5		Q5XXA6-1

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73517

AN:

151974

Hom.:

18619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.716

Gnomad SAS

AF:

0.528

Gnomad FIN

AF:

0.634

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.462

GnomAD2 exomes

AF:

0.541

AC:

134416

AN:

248316

AF XY:

0.540

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.555

Gnomad ASJ exome

AF:

0.523

Gnomad EAS exome

AF:

0.701

Gnomad FIN exome

AF:

0.636

Gnomad NFE exome

AF:

0.531

Gnomad OTH exome

AF:

0.525

GnomAD4 exome

AF:

0.527

AC:

769024

AN:

1459798

Hom.:

205274

Cov.:

AF XY:

0.527

AC XY:

382995

AN XY:

726252

show subpopulations

African (AFR)

AF:

0.330

AC:

11025

AN:

33446

American (AMR)

AF:

0.549

AC:

24532

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

13681

AN:

26118

East Asian (EAS)

AF:

0.761

AC:

30195

AN:

39688

South Asian (SAS)

AF:

0.515

AC:

44359

AN:

86202

European-Finnish (FIN)

AF:

0.633

AC:

33669

AN:

53192

Middle Eastern (MID)

AF:

0.444

AC:

2556

AN:

5762

European-Non Finnish (NFE)

AF:

0.520

AC:

577829

AN:

1110364

Other (OTH)

AF:

0.517

AC:

31178

AN:

60318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

18527

37053

55580

74106

92633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16576

33152

49728

66304

82880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.484

AC:

73564

AN:

152092

Hom.:

18620

Cov.:

AF XY:

0.489

AC XY:

36389

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.340

AC:

14114

AN:

41486

American (AMR)

AF:

0.486

AC:

7432

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1803

AN:

3470

East Asian (EAS)

AF:

0.716

AC:

3704

AN:

5170

South Asian (SAS)

AF:

0.530

AC:

2555

AN:

4818

European-Finnish (FIN)

AF:

0.634

AC:

6716

AN:

10600

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.525

AC:

35705

AN:

67948

Other (OTH)

AF:

0.456

AC:

964

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1935

3870

5806

7741

9676

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.513

Hom.:

3782

Bravo

AF:

0.467

Asia WGS

AF:

0.608

AC:

2113

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.9

(source)

DANN

Benign

0.30

PhyloP100

0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over