chr10-97744713-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001385875.1(ZFYVE27):c.269-16G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000645 in 1,612,980 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00060 ( 5 hom. )
Consequence
ZFYVE27
NM_001385875.1 splice_polypyrimidine_tract, intron
NM_001385875.1 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.201
Genes affected
ZFYVE27 (HGNC:26559): (zinc finger FYVE-type containing 27) This gene encodes a protein with several transmembrane domains, a Rab11-binding domain and a lipid-binding FYVE finger domain. The encoded protein appears to promote neurite formation. A mutation in this gene has been reported to be associated with hereditary spastic paraplegia, however the pathogenicity of the mutation, which may simply represent a polymorphism, is unclear. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 10-97744713-G-A is Benign according to our data. Variant chr10-97744713-G-A is described in ClinVar as [Benign]. Clinvar id is 1586409.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00111 (169/152402) while in subpopulation EAS AF= 0.0252 (131/5192). AF 95% confidence interval is 0.0217. There are 0 homozygotes in gnomad4. There are 85 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 169 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFYVE27 | NM_001385875.1 | c.269-16G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000684270.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFYVE27 | ENST00000684270.1 | c.269-16G>A | splice_polypyrimidine_tract_variant, intron_variant | NM_001385875.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00111 AC: 169AN: 152284Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00213 AC: 533AN: 250344Hom.: 8 AF XY: 0.00201 AC XY: 272AN XY: 135322
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GnomAD4 exome AF: 0.000596 AC: 871AN: 1460578Hom.: 5 Cov.: 30 AF XY: 0.000574 AC XY: 417AN XY: 726572
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 24, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at