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GeneBe

16-4650417-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_015246.4(MGRN1):c.141C>A(p.Pro47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,614,084 control chromosomes in the GnomAD database, including 222 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 107 hom., cov: 32)
Exomes 𝑓: 0.0024 ( 115 hom. )

Consequence

MGRN1
NM_015246.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.67
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-4650417-C-A is Benign according to our data. Variant chr16-4650417-C-A is described in ClinVar as [Benign]. Clinvar id is 782014.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.67 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MGRN1NM_015246.4 linkuse as main transcriptc.141C>A p.Pro47= synonymous_variant 2/17 ENST00000262370.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MGRN1ENST00000262370.12 linkuse as main transcriptc.141C>A p.Pro47= synonymous_variant 2/171 NM_015246.4 A1O60291-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0206
AC:
3134
AN:
152194
Hom.:
102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0710
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00655
Gnomad ASJ
AF:
0.0141
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.0144
GnomAD3 exomes
AF:
0.00555
AC:
1385
AN:
249418
Hom.:
50
AF XY:
0.00423
AC XY:
572
AN XY:
135318
show subpopulations
Gnomad AFR exome
AF:
0.0729
Gnomad AMR exome
AF:
0.00296
Gnomad ASJ exome
AF:
0.0106
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000229
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000238
Gnomad OTH exome
AF:
0.00215
GnomAD4 exome
AF:
0.00240
AC:
3511
AN:
1461774
Hom.:
115
Cov.:
32
AF XY:
0.00206
AC XY:
1500
AN XY:
727172
show subpopulations
Gnomad4 AFR exome
AF:
0.0778
Gnomad4 AMR exome
AF:
0.00342
Gnomad4 ASJ exome
AF:
0.0104
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000267
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000107
Gnomad4 OTH exome
AF:
0.00533
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0207
AC:
3159
AN:
152310
Hom.:
107
Cov.:
32
AF XY:
0.0204
AC XY:
1520
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0714
Gnomad4 AMR
AF:
0.00654
Gnomad4 ASJ
AF:
0.0141
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.00925
Hom.:
18
Bravo
AF:
0.0236
Asia WGS
AF:
0.00895
AC:
32
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000356

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
Cadd
Benign
1.8
Dann
Benign
0.82
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35046817; hg19: chr16-4700418; API