2-73519852-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001378454.1(ALMS1):c.9617C>T(p.Thr3206Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000182 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T3206A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378454.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALMS1 | NM_001378454.1 | c.9617C>T | p.Thr3206Ile | missense_variant | 11/23 | ENST00000613296.6 | |
ALMS1 | NM_015120.4 | c.9620C>T | p.Thr3207Ile | missense_variant | 11/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALMS1 | ENST00000613296.6 | c.9617C>T | p.Thr3206Ile | missense_variant | 11/23 | 1 | NM_001378454.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000341 AC: 85AN: 249342Hom.: 0 AF XY: 0.000407 AC XY: 55AN XY: 135280
GnomAD4 exome AF: 0.000170 AC: 248AN: 1461762Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 146AN XY: 727182
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74448
ClinVar
Submissions by phenotype
Alstrom syndrome Benign:3
Likely benign, criteria provided, single submitter | research | Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar | Oct 26, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 23, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | 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