rs55889738
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-T
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001378454.1(ALMS1):c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA(p.Glu17_Glu25del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 701,276 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
ALMS1
NM_001378454.1 disruptive_inframe_deletion
NM_001378454.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.45
Publications
7 publications found
Genes affected
ALMS1 (HGNC:428): (ALMS1 centrosome and basal body associated protein) This gene encodes a protein containing a large tandem-repeat domain as well as additional low complexity regions. The encoded protein functions in microtubule organization, particularly in the formation and maintanance of cilia. Mutations in this gene cause Alstrom syndrome. There is a pseudogene for this gene located adjacent in the same region of chromosome 2. Alternative splice variants have been described but their full length nature has not been determined. [provided by RefSeq, Apr 2014]
ALMS1 Gene-Disease associations (from GenCC):
- Alstrom syndromeInheritance: AR, Unknown Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001378454.1
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001378454.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ALMS1 | MANE Select | c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA | p.Glu17_Glu25del | disruptive_inframe_deletion | Exon 1 of 23 | NP_001365383.1 | Q8TCU4-1 | ||
| ALMS1 | c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA | p.Glu17_Glu25del | disruptive_inframe_deletion | Exon 1 of 23 | NP_055935.4 | Q8TCU4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ALMS1 | TSL:1 MANE Select | c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA | p.Glu17_Glu25del | disruptive_inframe_deletion | Exon 1 of 23 | ENSP00000482968.1 | Q8TCU4-1 | ||
| ALMS1 | TSL:1 | c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA | p.Glu17_Glu25del | disruptive_inframe_deletion | Exon 1 of 22 | ENSP00000478155.1 | A0A087WTU9 | ||
| ALMS1 | TSL:5 | c.48_74delGGAGGAGGAGGAGGAGGAGGAGGAGGA | p.Glu17_Glu25del | disruptive_inframe_deletion | Exon 1 of 16 | ENSP00000479094.1 | A0A087WV20 |
Frequencies
GnomAD3 genomes 0.00000697 AC: 1AN: 143532Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
143532
Hom.:
Cov.:
0
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: 0.0000143 AC: 8AN: 557744Hom.: 0 AF XY: 0.0000101 AC XY: 3AN XY: 297830 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
557744
Hom.:
AF XY:
AC XY:
3
AN XY:
297830
show subpopulations
African (AFR)
AF:
AC:
0
AN:
15796
American (AMR)
AF:
AC:
0
AN:
31236
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17646
East Asian (EAS)
AF:
AC:
0
AN:
30670
South Asian (SAS)
AF:
AC:
0
AN:
55946
European-Finnish (FIN)
AF:
AC:
0
AN:
36320
Middle Eastern (MID)
AF:
AC:
0
AN:
2422
European-Non Finnish (NFE)
AF:
AC:
8
AN:
337588
Other (OTH)
AF:
AC:
0
AN:
30120
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
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>80
Age
GnomAD4 genome 0.00000697 AC: 1AN: 143532Hom.: 0 Cov.: 0 AF XY: 0.0000144 AC XY: 1AN XY: 69544 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
143532
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
69544
show subpopulations
African (AFR)
AF:
AC:
0
AN:
39854
American (AMR)
AF:
AC:
0
AN:
14682
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3322
East Asian (EAS)
AF:
AC:
0
AN:
4598
South Asian (SAS)
AF:
AC:
0
AN:
4270
European-Finnish (FIN)
AF:
AC:
0
AN:
9398
Middle Eastern (MID)
AF:
AC:
0
AN:
282
European-Non Finnish (NFE)
AF:
AC:
1
AN:
64346
Other (OTH)
AF:
AC:
0
AN:
1954
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
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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