2-208273573-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015040.4(PIKFYVE):c.173-11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00261 in 1,614,098 control chromosomes in the GnomAD database, including 204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015040.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00300 AC: 457AN: 152146Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.0131 AC: 3283AN: 251356Hom.: 176 AF XY: 0.00960 AC XY: 1305AN XY: 135876
GnomAD4 exome AF: 0.00257 AC: 3755AN: 1461834Hom.: 192 Cov.: 31 AF XY: 0.00210 AC XY: 1528AN XY: 727226
GnomAD4 genome AF: 0.00301 AC: 458AN: 152264Hom.: 12 Cov.: 33 AF XY: 0.00312 AC XY: 232AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Fleck corneal dystrophy Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at