rs375436336
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001378454.1(ALMS1):c.10038C>T(p.Ser3346=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,120 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 (★★). Synonymous variant affecting the same amino acid position (i.e. S3346S) has been classified as Likely benign.
Frequency
Consequence
NM_001378454.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALMS1 | NM_001378454.1 | c.10038C>T | p.Ser3346= | synonymous_variant | 13/23 | ENST00000613296.6 | |
ALMS1 | NM_015120.4 | c.10041C>T | p.Ser3347= | synonymous_variant | 13/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALMS1 | ENST00000613296.6 | c.10038C>T | p.Ser3346= | synonymous_variant | 13/23 | 1 | NM_001378454.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000842 AC: 21AN: 249346Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135266
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727220
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74460
ClinVar
Submissions by phenotype
Alstrom syndrome Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2020 | 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