22-35317938-C-T
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The ENST00000449058.7(TOM1):c.114C>T(p.Asp38Asp) variant causes a synonymous change. The variant allele was found at a frequency of 0.00261 in 1,614,132 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 47 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 54 hom. )
Consequence
TOM1
ENST00000449058.7 synonymous
ENST00000449058.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.17
Genes affected
TOM1 (HGNC:11982): (target of myb1 membrane trafficking protein) This gene was identified as a target of the v-myb oncogene. The encoded protein shares its N-terminal domain in common with proteins associated with vesicular trafficking at the endosome. It is recruited to the endosomes by its interaction with endofin. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 22-35317938-C-T is Benign according to our data. Variant chr22-35317938-C-T is described in ClinVar as [Benign]. Clinvar id is 778918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0142 (2159/152278) while in subpopulation AFR AF= 0.0494 (2054/41550). AF 95% confidence interval is 0.0477. There are 47 homozygotes in gnomad4. There are 1004 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2159 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TOM1 | NM_005488.3 | c.114C>T | p.Asp38Asp | synonymous_variant | 2/15 | ENST00000449058.7 | NP_005479.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TOM1 | ENST00000449058.7 | c.114C>T | p.Asp38Asp | synonymous_variant | 2/15 | 1 | NM_005488.3 | ENSP00000394466.2 |
Frequencies
GnomAD3 genomes AF: 0.0141 AC: 2153AN: 152160Hom.: 47 Cov.: 32
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GnomAD3 exomes AF: 0.00366 AC: 920AN: 251482Hom.: 23 AF XY: 0.00259 AC XY: 352AN XY: 135912
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GnomAD4 exome AF: 0.00141 AC: 2058AN: 1461854Hom.: 54 Cov.: 31 AF XY: 0.00126 AC XY: 913AN XY: 727234
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GnomAD4 genome AF: 0.0142 AC: 2159AN: 152278Hom.: 47 Cov.: 32 AF XY: 0.0135 AC XY: 1004AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 01, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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