14-104708663-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_022489.4(INF2):c.1888-8T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_022489.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 148550Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248762Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135166
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460578Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 726564
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000202 AC: 3AN: 148550Hom.: 0 Cov.: 33 AF XY: 0.0000277 AC XY: 2AN XY: 72330
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at