rs759799299
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001378454.1(ALMS1):βc.9112_9114delβ(p.Pro3038del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ). Synonymous variant affecting the same amino acid position (i.e. T3036T) has been classified as Likely benign.
Frequency
Consequence
NM_001378454.1 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALMS1 | NM_001378454.1 | c.9112_9114del | p.Pro3038del | inframe_deletion | 10/23 | ENST00000613296.6 | |
ALMS1 | NM_015120.4 | c.9115_9117del | p.Pro3039del | inframe_deletion | 10/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALMS1 | ENST00000613296.6 | c.9112_9114del | p.Pro3038del | inframe_deletion | 10/23 | 1 | NM_001378454.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249318Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135262
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461850Hom.: 0 AF XY: 0.0000440 AC XY: 32AN XY: 727210
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
Alstrom syndrome Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 27, 2017 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 24, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 18, 2021 | This variant, c.9115_9117del, results in the deletion of 1 amino acid(s) of the ALMS1 protein (p.Pro3039del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs759799299, ExAC 0.004%). This variant has not been reported in the literature in individuals affected with ALMS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 555655). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at