chr5-80437866-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001284236.3(ZFYVE16):c.1181G>A(p.Arg394Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,613,906 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R394W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001284236.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE16 | NM_001284236.3 | c.1181G>A | p.Arg394Gln | missense_variant | 4/19 | ENST00000505560.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE16 | ENST00000505560.5 | c.1181G>A | p.Arg394Gln | missense_variant | 4/19 | 1 | NM_001284236.3 | P1 | |
FAM151B-DT | ENST00000666568.1 | n.259-23399C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0109 AC: 1650AN: 151998Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.00256 AC: 642AN: 250830Hom.: 7 AF XY: 0.00190 AC XY: 258AN XY: 135556
GnomAD4 exome AF: 0.00100 AC: 1468AN: 1461790Hom.: 20 Cov.: 67 AF XY: 0.000847 AC XY: 616AN XY: 727188
GnomAD4 genome AF: 0.0109 AC: 1663AN: 152116Hom.: 32 Cov.: 32 AF XY: 0.0107 AC XY: 795AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at