rs1851328
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020814.3(MARCHF4):c.517-32080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,950 control chromosomes in the GnomAD database, including 12,992 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 0.40 ( 12992 hom., cov: 32)
Consequence
MARCHF4
NM_020814.3 intron
NM_020814.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.313
Genes affected
MARCHF4 (HGNC:29269): (membrane associated ring-CH-type finger 4) MARCH4 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. MARCH4 reduces surface accumulation of several membrane glycoproteins by directing them to the endosomal compartment (Bartee et al., 2004 [PubMed 14722266]).[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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MARCHF4 | NM_020814.3 | c.517-32080G>A | intron_variant | ENST00000273067.5 | |||
LOC107985983 | XR_001739877.2 | n.353-2269C>T | intron_variant, non_coding_transcript_variant | ||||
LOC107985983 | XR_001739876.2 | n.353-2269C>T | intron_variant, non_coding_transcript_variant | ||||
LOC107985983 | XR_001739878.2 | n.348-2269C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MARCHF4 | ENST00000273067.5 | c.517-32080G>A | intron_variant | 1 | NM_020814.3 | P1 | |||
ENST00000452736.1 | n.336-2269C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.400 AC: 60661AN: 151832Hom.: 12987 Cov.: 32
GnomAD3 genomes
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60661
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.399 AC: 60691AN: 151950Hom.: 12992 Cov.: 32 AF XY: 0.405 AC XY: 30098AN XY: 74248
GnomAD4 genome
?
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60691
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151950
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32
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30098
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74248
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1450
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at