16-4673551-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015246.4(MGRN1):c.849C>T(p.Ser283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00576 in 1,613,730 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0059 ( 32 hom. )
Consequence
MGRN1
NM_015246.4 synonymous
NM_015246.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.14
Genes affected
MGRN1 (HGNC:20254): (mahogunin ring finger 1) Enables ubiquitin-protein transferase activity. Involved in endosome to lysosome transport; negative regulation of signal transduction; and protein monoubiquitination. Located in several cellular components, including early endosome; endoplasmic reticulum; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 16-4673551-C-T is Benign according to our data. Variant chr16-4673551-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646155.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-5.14 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGRN1 | NM_015246.4 | c.849C>T | p.Ser283= | synonymous_variant | 10/17 | ENST00000262370.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGRN1 | ENST00000262370.12 | c.849C>T | p.Ser283= | synonymous_variant | 10/17 | 1 | NM_015246.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00454 AC: 691AN: 152164Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.00389 AC: 975AN: 250684Hom.: 2 AF XY: 0.00422 AC XY: 572AN XY: 135588
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GnomAD4 exome AF: 0.00589 AC: 8607AN: 1461448Hom.: 32 Cov.: 33 AF XY: 0.00584 AC XY: 4245AN XY: 727060
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GnomAD4 genome AF: 0.00454 AC: 691AN: 152282Hom.: 6 Cov.: 33 AF XY: 0.00419 AC XY: 312AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | MGRN1: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at