rs13158763

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001102562.3(MARCHF11):​c.694-2440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,714 control chromosomes in the GnomAD database, including 7,907 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 0.30 ( 7907 hom., cov: 31)

Consequence

MARCHF11
NM_001102562.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.314
Variant links:
Genes affected
MARCHF11 (HGNC:33609): (membrane associated ring-CH-type finger 11) MARCH11 is a member of the MARCH family of membrane-bound E3 ubiquitin ligases (EC 6.3.2.19). These enzymes add ubiquitin (see MIM 191339) to target lysines in substrate proteins, thereby signaling their intracellular transport. March11 appears to have a role in ubiquitin-mediated protein sorting in the trans-Golgi network (TGN)-multivesicular body (MVB) transport pathway (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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MARCHF11NM_001102562.3 linkc.694-2440C>T intron_variant ENST00000332432.9 NP_001096032.1
MARCHF11XM_047417230.1 linkc.694-25728C>T intron_variant XP_047273186.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MARCHF11ENST00000332432.9 linkc.694-2440C>T intron_variant 5 NM_001102562.3 ENSP00000333181.7 A6NNE9-1
MARCHF11ENST00000507111.1 linkc.103-25728C>T intron_variant 3 ENSP00000424425.1 H0Y9K6
MARCHF11ENST00000505509.1 linkn.275-2440C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.299
AC:
45311
AN:
151596
Hom.:
7896
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.169
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.440
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.565
Gnomad SAS
AF:
0.503
Gnomad FIN
AF:
0.476
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.303
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.299
AC:
45348
AN:
151714
Hom.:
7907
Cov.:
31
AF XY:
0.312
AC XY:
23153
AN XY:
74094
show subpopulations
Gnomad4 AFR
AF:
0.169
Gnomad4 AMR
AF:
0.441
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.564
Gnomad4 SAS
AF:
0.503
Gnomad4 FIN
AF:
0.476
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.301
Alfa
AF:
0.316
Hom.:
1471
Bravo
AF:
0.289
Asia WGS
AF:
0.467
AC:
1623
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.1
DANN
Benign
0.43

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: rs13158763; hg19: chr5-16093630; API