chr16-632667-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_053284.3(WFIKKN1):c.257C>T(p.Ala86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,604,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_053284.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000257 AC: 6AN: 233714Hom.: 0 AF XY: 0.0000313 AC XY: 4AN XY: 127662
GnomAD4 exome AF: 0.0000207 AC: 30AN: 1451866Hom.: 0 Cov.: 32 AF XY: 0.0000166 AC XY: 12AN XY: 721400
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.257C>T (p.A86V) alteration is located in exon 2 (coding exon 2) of the WFIKKN1 gene. This alteration results from a C to T substitution at nucleotide position 257, causing the alanine (A) at amino acid position 86 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at