NM_001025356.3:c.102C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001025356.3(ANO6):c.102C>T(p.Pro34Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00862 in 1,613,810 control chromosomes in the GnomAD database, including 927 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.044 ( 479 hom., cov: 33)
Exomes 𝑓: 0.0049 ( 448 hom. )
Consequence
ANO6
NM_001025356.3 synonymous
NM_001025356.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.338
Publications
5 publications found
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 syndromeInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 12-45302045-C-T is Benign according to our data. Variant chr12-45302045-C-T is described in ClinVar as [Benign]. Clinvar id is 257139.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.338 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0439 AC: 6677AN: 152022Hom.: 479 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
6677
AN:
152022
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0121 AC: 3037AN: 251294 AF XY: 0.00826 show subpopulations
GnomAD2 exomes
AF:
AC:
3037
AN:
251294
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00493 AC: 7211AN: 1461670Hom.: 448 Cov.: 32 AF XY: 0.00422 AC XY: 3065AN XY: 727140 show subpopulations
GnomAD4 exome
AF:
AC:
7211
AN:
1461670
Hom.:
Cov.:
32
AF XY:
AC XY:
3065
AN XY:
727140
show subpopulations
African (AFR)
AF:
AC:
5312
AN:
33466
American (AMR)
AF:
AC:
440
AN:
44706
Ashkenazi Jewish (ASJ)
AF:
AC:
32
AN:
26124
East Asian (EAS)
AF:
AC:
1
AN:
39690
South Asian (SAS)
AF:
AC:
81
AN:
86258
European-Finnish (FIN)
AF:
AC:
14
AN:
53416
Middle Eastern (MID)
AF:
AC:
63
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
580
AN:
1111864
Other (OTH)
AF:
AC:
688
AN:
60380
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
331
662
992
1323
1654
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
170
340
510
680
850
<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: 0.0440 AC: 6699AN: 152140Hom.: 479 Cov.: 33 AF XY: 0.0422 AC XY: 3141AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
6699
AN:
152140
Hom.:
Cov.:
33
AF XY:
AC XY:
3141
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
6163
AN:
41460
American (AMR)
AF:
AC:
396
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5182
South Asian (SAS)
AF:
AC:
2
AN:
4826
European-Finnish (FIN)
AF:
AC:
2
AN:
10594
Middle Eastern (MID)
AF:
AC:
6
AN:
294
European-Non Finnish (NFE)
AF:
AC:
53
AN:
68022
Other (OTH)
AF:
AC:
74
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
291
582
873
1164
1455
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
62
124
186
248
310
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
34
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Jan 29, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Nov 10, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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