rs2251393
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152598.4(MARCHF10):c.*132C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 1,571,044 control chromosomes in the GnomAD database, including 570,887 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.81 ( 50770 hom., cov: 32)
Exomes 𝑓: 0.86 ( 520117 hom. )
Consequence
MARCHF10
NM_152598.4 3_prime_UTR
NM_152598.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.322
Genes affected
MARCHF10 (HGNC:26655): (membrane associated ring-CH-type finger 10) MARCH10 is a member of the MARCH family of membrane-bound E3 ubiquitin ligases (EC 6.3.2.19). MARCH enzymes add ubiquitin (see MIM 191339) to target lysines in substrate proteins, thereby signaling their vesicular transport between membrane compartments (Morokuma et al., 2007 [PubMed 17604280]).[supplied by OMIM, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MARCHF10 | NM_152598.4 | c.*132C>T | 3_prime_UTR_variant | 11/11 | ENST00000311269.10 | NP_689811.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MARCHF10 | ENST00000311269.10 | c.*132C>T | 3_prime_UTR_variant | 11/11 | 2 | NM_152598.4 | ENSP00000311496 | P2 |
Frequencies
GnomAD3 genomes AF: 0.813 AC: 123575AN: 152050Hom.: 50766 Cov.: 32
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GnomAD3 exomes AF: 0.846 AC: 191793AN: 226626Hom.: 81532 AF XY: 0.851 AC XY: 104738AN XY: 123042
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GnomAD4 exome AF: 0.855 AC: 1213593AN: 1418876Hom.: 520117 Cov.: 29 AF XY: 0.856 AC XY: 602502AN XY: 703896
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GnomAD4 genome AF: 0.812 AC: 123627AN: 152168Hom.: 50770 Cov.: 32 AF XY: 0.815 AC XY: 60640AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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