chr14-72998065-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021260.4(ZFYVE1):āc.734A>Gā(p.Asn245Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,884 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_021260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFYVE1 | NM_021260.4 | c.734A>G | p.Asn245Ser | missense_variant | 3/12 | ENST00000556143.6 | NP_067083.1 | |
ZFYVE1 | NM_001281734.2 | c.734A>G | p.Asn245Ser | missense_variant | 3/12 | NP_001268663.1 | ||
ZFYVE1 | XM_047431481.1 | c.734A>G | p.Asn245Ser | missense_variant | 3/7 | XP_047287437.1 | ||
ZFYVE1 | XM_047431482.1 | c.-512A>G | 5_prime_UTR_variant | 3/12 | XP_047287438.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFYVE1 | ENST00000556143.6 | c.734A>G | p.Asn245Ser | missense_variant | 3/12 | 1 | NM_021260.4 | ENSP00000450742.1 | ||
ZFYVE1 | ENST00000318876.9 | c.734A>G | p.Asn245Ser | missense_variant | 3/12 | 1 | ENSP00000326921.5 | |||
ZFYVE1 | ENST00000553891.5 | c.734A>G | p.Asn245Ser | missense_variant | 3/13 | 5 | ENSP00000452442.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727242
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 08, 2024 | The c.734A>G (p.N245S) alteration is located in exon 3 (coding exon 2) of the ZFYVE1 gene. This alteration results from a A to G substitution at nucleotide position 734, causing the asparagine (N) at amino acid position 245 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.