rs879255406
Positions:
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGA-T
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGA-T
- chr2-73385903-TGGAGGAGGA-T
- chr2-73385903-TGGAGGAGGAGGAGGA-T
- chr2-73385903-T-TGGAGGAGGAGGA
- chr2-73385903-T-TGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-T-TGGA
- chr2-73385903-TGGAGGAGGAGGA-T
- chr2-73385903-TGGA-T
- chr2-73385903-TGGAGGAGGAGGAGGAGGAGGAGGAGGA-T
- chr2-73385903-T-TGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-T-TGGAGGA
- chr2-73385903-T-TGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGAGGAGGAGGAGGA-T
- chr2-73385903-T-TGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr2-73385903-TGGAGGA-T
- chr2-73385903-T-TGGAGGAGGA
- chr2-73385903-T-TGGAGGAGGAGGAGGAGGA
- chr2-73385903-T-TGGAGGAGGAGGAGGAGGAGGAGGA
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_001378454.1(ALMS1):c.54_74del(p.Glu22_Glu28del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 701,370 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000042 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000043 ( 0 hom. )
Consequence
ALMS1
NM_001378454.1 inframe_deletion
NM_001378454.1 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.45
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_001378454.1
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| ALMS1 | NM_001378454.1 | c.54_74del | p.Glu22_Glu28del | inframe_deletion | 1/23 | ENST00000613296.6 | |
| ALMS1 | NM_015120.4 | c.54_74del | p.Glu23_Glu29del | inframe_deletion | 1/23 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ALMS1 | ENST00000613296.6 | c.54_74del | p.Glu22_Glu28del | inframe_deletion | 1/23 | 1 | NM_001378454.1 | P3 |
Frequencies
GnomAD3 genomes 0.0000418 AC: 6AN: 143530Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000430 AC: 24AN: 557736Hom.: 0 AF XY: 0.0000504 AC XY: 15AN XY: 297828
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GnomAD4 genome 0.0000418 AC: 6AN: 143634Hom.: 0 Cov.: 0 AF XY: 0.0000574 AC XY: 4AN XY: 69662
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Alstrom syndrome Uncertain:3Benign:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 22, 2022 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jan 17, 2017 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Aug 07, 2018 | - - |
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at