rs771463400
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001082538.3(TCTN1):c.473-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000146 in 1,580,000 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
TCTN1
NM_001082538.3 intron
NM_001082538.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.239
Publications
0 publications found
Genes affected
TCTN1 (HGNC:26113): (tectonic family member 1) This gene encodes a member of a family of secreted and transmembrane proteins. The orthologous gene in mouse functions downstream of smoothened and rab23 to modulate hedgehog signal transduction. This protein is a component of the tectonic-like complex, which forms a barrier between the ciliary axoneme and the basal body. A mutation in this gene was found in a family with Joubert syndrome-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
HVCN1 (HGNC:28240): (hydrogen voltage gated channel 1) This gene encodes a voltage-gated protein channel protein expressed more highly in certain cells of the immune system. Phagocytic cells produce superoxide anions which require this channel protein, and in B cells this same process facilitates antibody production. This same channel protein, however, can also regulate functions in other cells including spermatozoa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-110628749-GT-G is Benign according to our data. Variant chr12-110628749-GT-G is described in ClinVar as Benign. ClinVar VariationId is 1608758.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001082538.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TCTN1 | TSL:1 MANE Select | c.473-17delT | intron | N/A | ENSP00000380779.4 | Q2MV58-2 | |||
| TCTN1 | TSL:1 | c.473-17delT | intron | N/A | ENSP00000448735.1 | Q2MV58-1 | |||
| TCTN1 | TSL:1 | c.473-17delT | intron | N/A | ENSP00000380775.3 | Q2MV58-3 |
Frequencies
GnomAD3 genomes 0.0000198 AC: 3AN: 151704Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151704
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000427 AC: 10AN: 234146 AF XY: 0.0000548 show subpopulations
GnomAD2 exomes
AF:
AC:
10
AN:
234146
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000140 AC: 20AN: 1428180Hom.: 0 Cov.: 29 AF XY: 0.0000168 AC XY: 12AN XY: 712254 show subpopulations
GnomAD4 exome
AF:
AC:
20
AN:
1428180
Hom.:
Cov.:
29
AF XY:
AC XY:
12
AN XY:
712254
show subpopulations
African (AFR)
AF:
AC:
1
AN:
32716
American (AMR)
AF:
AC:
8
AN:
44284
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25862
East Asian (EAS)
AF:
AC:
0
AN:
39374
South Asian (SAS)
AF:
AC:
3
AN:
85132
European-Finnish (FIN)
AF:
AC:
0
AN:
49126
Middle Eastern (MID)
AF:
AC:
1
AN:
5414
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1086950
Other (OTH)
AF:
AC:
1
AN:
59322
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
1
2
4
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6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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>80
Age
GnomAD4 genome 0.0000198 AC: 3AN: 151820Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74214 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151820
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74214
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41460
American (AMR)
AF:
AC:
3
AN:
15138
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5180
South Asian (SAS)
AF:
AC:
0
AN:
4810
European-Finnish (FIN)
AF:
AC:
0
AN:
10544
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67904
Other (OTH)
AF:
AC:
0
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Meckel-Gruber syndrome;C5979921:Joubert syndrome (1)
-
-
1
TCTN1-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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