NM_001134831.2:c.1912+135A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001134831.2(AHI1):c.1912+135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 960,342 control chromosomes in the GnomAD database, including 465,350 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.99 ( 74315 hom., cov: 33)
Exomes 𝑓: 0.98 ( 391035 hom. )
Consequence
AHI1
NM_001134831.2 intron
NM_001134831.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.706
Publications
0 publications found
Genes affected
AHI1 (HGNC:21575): (Abelson helper integration site 1) This gene is apparently required for both cerebellar and cortical development in humans. This gene mutations cause specific forms of Joubert syndrome-related disorders. Joubert syndrome (JS) is a recessively inherited developmental brain disorder with several identified causative chromosomal loci. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]
AHI1 Gene-Disease associations (from GenCC):
- Joubert syndrome 3Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Laboratory for Molecular Medicine, Ambry Genetics
- Joubert syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndrome with ocular defectInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- retinitis pigmentosaInheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 6-135442447-T-C is Benign according to our data. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-135442447-T-C is described in CliVar as Benign. Clinvar id is 1246420.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.988 AC: 150336AN: 152208Hom.: 74257 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
150336
AN:
152208
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:
GnomAD4 exome AF: 0.984 AC: 794909AN: 808016Hom.: 391035 AF XY: 0.984 AC XY: 387075AN XY: 393452 show subpopulations
GnomAD4 exome
AF:
AC:
794909
AN:
808016
Hom.:
AF XY:
AC XY:
387075
AN XY:
393452
show subpopulations
African (AFR)
AF:
AC:
17867
AN:
17912
American (AMR)
AF:
AC:
11799
AN:
11882
Ashkenazi Jewish (ASJ)
AF:
AC:
13696
AN:
13828
East Asian (EAS)
AF:
AC:
28894
AN:
28894
South Asian (SAS)
AF:
AC:
21564
AN:
21700
European-Finnish (FIN)
AF:
AC:
35661
AN:
36224
Middle Eastern (MID)
AF:
AC:
2744
AN:
2770
European-Non Finnish (NFE)
AF:
AC:
627519
AN:
639182
Other (OTH)
AF:
AC:
35165
AN:
35624
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
619
1238
1858
2477
3096
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
12412
24824
37236
49648
62060
<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: 0.988 AC: 150453AN: 152326Hom.: 74315 Cov.: 33 AF XY: 0.988 AC XY: 73596AN XY: 74484 show subpopulations
GnomAD4 genome
AF:
AC:
150453
AN:
152326
Hom.:
Cov.:
33
AF XY:
AC XY:
73596
AN XY:
74484
show subpopulations
African (AFR)
AF:
AC:
41368
AN:
41574
American (AMR)
AF:
AC:
15207
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
3443
AN:
3470
East Asian (EAS)
AF:
AC:
5186
AN:
5188
South Asian (SAS)
AF:
AC:
4802
AN:
4830
European-Finnish (FIN)
AF:
AC:
10490
AN:
10620
Middle Eastern (MID)
AF:
AC:
291
AN:
294
European-Non Finnish (NFE)
AF:
AC:
66663
AN:
68024
Other (OTH)
AF:
AC:
2091
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
96
192
287
383
479
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
916
1832
2748
3664
4580
<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:
3466
AN:
3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 26, 2018
GeneDx
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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