14-103727866-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024071.4(ZFYVE21):c.310C>T(p.Leu104Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,613,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152244Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250166Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135628
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1460786Hom.: 0 Cov.: 48 AF XY: 0.0000633 AC XY: 46AN XY: 726734
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152244Hom.: 0 Cov.: 35 AF XY: 0.0000807 AC XY: 6AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.310C>T (p.L104F) alteration is located in exon 3 (coding exon 3) of the ZFYVE21 gene. This alteration results from a C to T substitution at nucleotide position 310, causing the leucine (L) at amino acid position 104 to be replaced by a phenylalanine (F). 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