16-4652820-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015246.4(MGRN1):c.439G>A(p.Ala147Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000542 in 1,604,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
MGRN1
NM_015246.4 missense
NM_015246.4 missense
Scores
2
13
Clinical Significance
Conservation
PhyloP100: 5.01
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.03996262).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGRN1 | NM_015246.4 | c.439G>A | p.Ala147Thr | missense_variant | 4/17 | ENST00000262370.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGRN1 | ENST00000262370.12 | c.439G>A | p.Ala147Thr | missense_variant | 4/17 | 1 | NM_015246.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152216Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000556 AC: 13AN: 233860Hom.: 0 AF XY: 0.0000626 AC XY: 8AN XY: 127782
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GnomAD4 exome AF: 0.0000379 AC: 55AN: 1451798Hom.: 0 Cov.: 31 AF XY: 0.0000347 AC XY: 25AN XY: 721102
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GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74484
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ExAC
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.439G>A (p.A147T) alteration is located in exon 4 (coding exon 4) of the MGRN1 gene. This alteration results from a G to A substitution at nucleotide position 439, causing the alanine (A) at amino acid position 147 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T;T;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Benign
T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
0.011, 0.0090, 0.014, 0.096
.;B;B;.;B;B;B;.
Vest4
0.45, 0.45, 0.48, 0.45
MVP
MPC
0.046
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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