rs199874928
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001378454.1(ALMS1):āc.11765A>Gā(p.Asn3922Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000144 in 1,614,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378454.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000184 AC: 46AN: 250424Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135760
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727242
GnomAD4 genome AF: 0.000735 AC: 112AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74506
ClinVar
Submissions by phenotype
Alstrom syndrome Benign:2Other:1
Potent mutations in ALMS1 are associated with a rare condition called Alstrom syndrome. It can cause excessive eating, insulin resistance. However, no evidence is found to ascertain the role of rs199874928 in Alstrom syndrome yet. -
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not specified Uncertain:1
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not provided Uncertain:1
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Monogenic diabetes Benign:1
ACMG criteria: PP3 (3 predictors), BP4 (7 predictors), BP1 (missense in gene with truncating cause disease)=likely benign -
Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at