Genetic Variant ANO6:p.Ala312Ala (chr12-45357362-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001025356.3(ANO6):c.936C>T(p.Ala312Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,613,956 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A312A) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0077 ( 13 hom., cov: 32)

Exomes 𝑓: 0.010 ( 93 hom. )

Consequence

ANO6
NM_001025356.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.597

Publications

3 publications found

Variant links:

Genes affected

ANO6 (HGNC:25240): (anoctamin 6) This gene encodes a multi-pass transmembrane protein that belongs to the anoctamin family. This protein is an essential component for the calcium-dependent exposure of phosphatidylserine on the cell surface. The scrambling of phospholipid occurs in various biological systems, such as when blood platelets are activated, they expose phosphatidylserine to trigger the clotting system. Mutations in this gene are associated with Scott syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

ANO6 Gene-Disease associations (from GenCC):

Scott syndrome
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet

ANO6 links:

ENSG00000293678 (HGNC:):

ENSG00000293678 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 12-45357362-C-T is Benign according to our data. Variant chr12-45357362-C-T is described in ClinVar as Benign. ClinVar VariationId is 257148.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.597 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00774 (1178/152286) while in subpopulation NFE AF = 0.0133 (903/68022). AF 95% confidence interval is 0.0126. There are 13 homozygotes in GnomAd4. There are 524 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 13 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025356.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANO6	NM_001025356.3	MANE Select	c.936C>T	p.Ala312Ala	synonymous	Exon 8 of 20	NP_001020527.2	Q4KMQ2-1
ANO6	NM_001204803.2		c.999C>T	p.Ala333Ala	synonymous	Exon 9 of 21	NP_001191732.1	Q4KMQ2-2
ANO6	NM_001142679.2		c.936C>T	p.Ala312Ala	synonymous	Exon 8 of 20	NP_001136151.1	Q4KMQ2-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANO6	ENST00000320560.13	TSL:1 MANE Select	c.936C>T	p.Ala312Ala	synonymous	Exon 8 of 20	ENSP00000320087.8	Q4KMQ2-1
ANO6	ENST00000423947.7	TSL:1	c.999C>T	p.Ala333Ala	synonymous	Exon 9 of 21	ENSP00000409126.3	Q4KMQ2-2
ANO6	ENST00000425752.6	TSL:1	c.936C>T	p.Ala312Ala	synonymous	Exon 8 of 20	ENSP00000391417.2	Q4KMQ2-4

Frequencies

GnomAD3 genomes

AF:

0.00775

AC:

1179

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00181

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00616

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.00861

GnomAD2 exomes

AF:

0.00798

AC:

2006

AN:

251398

AF XY:

0.00836

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00321

Gnomad ASJ exome

AF:

0.00476

Gnomad EAS exome

AF:

0.000218

Gnomad FIN exome

AF:

0.00642

Gnomad NFE exome

AF:

0.0132

Gnomad OTH exome

AF:

0.00832

GnomAD4 exome

AF:

0.0104

AC:

15217

AN:

1461670

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

7457

AN XY:

727138

show subpopulations

African (AFR)

AF:

0.00119

AC:

AN:

33478

American (AMR)

AF:

0.00313

AC:

140

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00494

AC:

129

AN:

26132

East Asian (EAS)

AF:

0.000151

AC:

AN:

39684

South Asian (SAS)

AF:

0.00464

AC:

400

AN:

86238

European-Finnish (FIN)

AF:

0.00766

AC:

409

AN:

53412

Middle Eastern (MID)

AF:

0.00370

AC:

AN:

5672

European-Non Finnish (NFE)

AF:

0.0121

AC:

13454

AN:

1111946

Other (OTH)

AF:

0.0102

AC:

618

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

803

1607

2410

3214

4017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.00774

AC:

1178

AN:

152286

Hom.:

Cov.:

AF XY:

0.00704

AC XY:

524

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.00180

AC:

AN:

41562

American (AMR)

AF:

0.00615

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00663

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.00373

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00433

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0133

AC:

903

AN:

68022

Other (OTH)

AF:

0.00852

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

114

170

227

284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0104

Hom.:

Bravo

AF:

0.00730

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0109

EpiControl

AF:

0.0119

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

0.052

(source)

DANN

Benign

0.54

PhyloP100

-0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=99/1

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over