X-111681212-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001099922.3(ALG13):c.-7C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000329 in 1,209,650 control chromosomes in the GnomAD database, including 1 homozygotes. There are 143 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001099922.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000328 AC: 37AN: 112696Hom.: 0 Cov.: 24 AF XY: 0.000516 AC XY: 18AN XY: 34852
GnomAD3 exomes AF: 0.000448 AC: 82AN: 182870Hom.: 0 AF XY: 0.000475 AC XY: 32AN XY: 67350
GnomAD4 exome AF: 0.000329 AC: 361AN: 1096898Hom.: 1 Cov.: 30 AF XY: 0.000345 AC XY: 125AN XY: 362300
GnomAD4 genome AF: 0.000328 AC: 37AN: 112752Hom.: 0 Cov.: 24 AF XY: 0.000515 AC XY: 18AN XY: 34918
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at