chr4-2304502-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020972.3(ZFYVE28):c.1838C>T(p.Ala613Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,612,468 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020972.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE28 | NM_020972.3 | c.1838C>T | p.Ala613Val | missense_variant | 8/13 | ENST00000290974.7 | |
ZFYVE28 | NM_001172656.2 | c.1748C>T | p.Ala583Val | missense_variant | 7/12 | ||
ZFYVE28 | NM_001172659.2 | c.1628C>T | p.Ala543Val | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE28 | ENST00000290974.7 | c.1838C>T | p.Ala613Val | missense_variant | 8/13 | 1 | NM_020972.3 | P2 | |
ENST00000510632.1 | n.263-2389G>A | intron_variant, non_coding_transcript_variant | 4 | ||||||
ZFYVE28 | ENST00000511071.5 | c.1748C>T | p.Ala583Val | missense_variant | 7/12 | 5 | A2 | ||
ZFYVE28 | ENST00000515312.5 | c.1628C>T | p.Ala543Val | missense_variant | 8/13 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000631 AC: 96AN: 152230Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000302 AC: 75AN: 248392Hom.: 1 AF XY: 0.000274 AC XY: 37AN XY: 135014
GnomAD4 exome AF: 0.000128 AC: 187AN: 1460120Hom.: 1 Cov.: 41 AF XY: 0.000135 AC XY: 98AN XY: 726226
GnomAD4 genome ? AF: 0.000630 AC: 96AN: 152348Hom.: 1 Cov.: 34 AF XY: 0.000698 AC XY: 52AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 31, 2023 | The c.1838C>T (p.A613V) alteration is located in exon 8 (coding exon 8) of the ZFYVE28 gene. This alteration results from a C to T substitution at nucleotide position 1838, causing the alanine (A) at amino acid position 613 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