chr7-38742254-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014396.4(VPS41):c.2123-133A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 817,620 control chromosomes in the GnomAD database, including 22,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5551 hom., cov: 32)
Exomes 𝑓: 0.21 ( 17035 hom. )
Consequence
VPS41
NM_014396.4 intron
NM_014396.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.31
Genes affected
VPS41 (HGNC:12713): (VPS41 subunit of HOPS complex) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]
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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=-0.59).
BP6
Variant 7-38742254-T-C is Benign according to our data. Variant chr7-38742254-T-C is described in ClinVar as [Benign]. Clinvar id is 1273568.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS41 | NM_014396.4 | c.2123-133A>G | intron_variant | ENST00000310301.9 | |||
VPS41 | NM_080631.4 | c.2048-133A>G | intron_variant | ||||
VPS41 | XM_017011988.2 | c.968-133A>G | intron_variant | ||||
VPS41 | XR_007060008.1 | n.2140-133A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS41 | ENST00000310301.9 | c.2123-133A>G | intron_variant | 1 | NM_014396.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.247 AC: 37618AN: 152008Hom.: 5536 Cov.: 32
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GnomAD4 exome AF: 0.207 AC: 138013AN: 665494Hom.: 17035 AF XY: 0.215 AC XY: 73338AN XY: 340978
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GnomAD4 genome AF: 0.248 AC: 37664AN: 152126Hom.: 5551 Cov.: 32 AF XY: 0.252 AC XY: 18720AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at