17-62736249-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_152598.4(MARCHF10):​c.1619C>T​(p.Ala540Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 0 hom. )

Consequence

MARCHF10
NM_152598.4 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.120
Variant links:
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]

Genome browser will be placed here

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=0.060979962).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MARCHF10NM_152598.4 linkc.1619C>T p.Ala540Val missense_variant Exon 6 of 11 ENST00000311269.10 NP_689811.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MARCHF10ENST00000311269.10 linkc.1619C>T p.Ala540Val missense_variant Exon 6 of 11 2 NM_152598.4 ENSP00000311496.5 Q8NA82

Frequencies

GnomAD3 genomes
AF:
0.000151
AC:
23
AN:
152188
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000115
AC:
29
AN:
251172
Hom.:
0
AF XY:
0.000103
AC XY:
14
AN XY:
135754
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000238
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000155
AC:
227
AN:
1461882
Hom.:
0
Cov.:
32
AF XY:
0.000161
AC XY:
117
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000200
Gnomad4 OTH exome
AF:
0.0000662
GnomAD4 genome
AF:
0.000151
AC:
23
AN:
152188
Hom.:
0
Cov.:
32
AF XY:
0.0000941
AC XY:
7
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000266
Hom.:
0
Bravo
AF:
0.000166
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.0000576
AC:
7
EpiCase
AF:
0.000164
EpiControl
AF:
0.000296

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Oct 06, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1619C>T (p.A540V) alteration is located in exon 6 (coding exon 5) of the MARCH10 gene. This alteration results from a C to T substitution at nucleotide position 1619, causing the alanine (A) at amino acid position 540 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.098
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
5.3
DANN
Benign
0.68
DEOGEN2
Benign
0.0016
.;T;T;.;.
Eigen
Benign
-0.96
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.029
N
LIST_S2
Benign
0.76
T;.;T;T;T
M_CAP
Benign
0.0057
T
MetaRNN
Benign
0.061
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.1
.;L;L;.;.
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.79
.;N;N;.;N
REVEL
Benign
0.033
Sift
Benign
0.049
.;D;D;.;T
Sift4G
Benign
0.20
T;T;T;T;T
Polyphen
0.45, 0.59
.;P;P;.;P
Vest4
0.038, 0.039, 0.057
MVP
0.17
MPC
0.13
ClinPred
0.038
T
GERP RS
-0.76
Varity_R
0.052
gMVP
0.15

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: rs138151992; hg19: chr17-60813610; API