12-85283702-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006982.3(ALX1):c.357T>A(p.Leu119Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000626 in 1,614,122 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006982.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000532 AC: 81AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000477 AC: 120AN: 251464Hom.: 0 AF XY: 0.000449 AC XY: 61AN XY: 135904
GnomAD4 exome AF: 0.000635 AC: 929AN: 1461870Hom.: 1 Cov.: 31 AF XY: 0.000611 AC XY: 444AN XY: 727240
GnomAD4 genome AF: 0.000532 AC: 81AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74442
ClinVar
Submissions by phenotype
ALX1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at