rs10496192
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378454.1(ALMS1):āc.6212T>Cā(p.Ile2071Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,613,212 control chromosomes in the GnomAD database, including 21,161 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001378454.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.138 AC: 20924AN: 152070Hom.: 1599 Cov.: 32
GnomAD3 exomes AF: 0.145 AC: 35804AN: 246918Hom.: 2864 AF XY: 0.147 AC XY: 19725AN XY: 134302
GnomAD4 exome AF: 0.161 AC: 234698AN: 1461024Hom.: 19561 Cov.: 38 AF XY: 0.161 AC XY: 117148AN XY: 726836
GnomAD4 genome AF: 0.138 AC: 20938AN: 152188Hom.: 1600 Cov.: 32 AF XY: 0.135 AC XY: 10074AN XY: 74412
ClinVar
Submissions by phenotype
not specified Benign:5
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p.Ile2070Thr in exon 8 of ALMS1: This variant is not expected to have clinical s ignificance because it has been identified in 16.61% (10786/64944) of European c hromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute .org; dbSNP rs10496192). -
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Alstrom syndrome Benign:3
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not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as 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