chr2-73448424-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001378454.1(ALMS1):c.1897C>T(p.Gln633*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,742 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Q633Q) has been classified as Benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001378454.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249038Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135110
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461742Hom.: 0 Cov.: 59 AF XY: 0.00000413 AC XY: 3AN XY: 727182
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Alstrom syndrome Pathogenic:1
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not provided Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at