21-41432752-G-A

Variant summary

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

The NM_002462.5(MX1):​c.105+577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,102 control chromosomes in the GnomAD database, including 33,657 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 0.64 ( 33657 hom., cov: 32)

Consequence

MX1
NM_002462.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225
Variant links:
Genes affected
MX1 (HGNC:7532): (MX dynamin like GTPase 1) This gene encodes a guanosine triphosphate (GTP)-metabolizing protein that participates in the cellular antiviral response. The encoded protein is induced by type I and type II interferons and antagonizes the replication process of several different RNA and DNA viruses. There is a related gene located adjacent to this gene on chromosome 21, and there are multiple pseudogenes located in a cluster on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MX1NM_002462.5 linkc.105+577G>A intron_variant ENST00000398598.8 NP_002453.2 P20591-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MX1ENST00000398598.8 linkc.105+577G>A intron_variant 1 NM_002462.5 ENSP00000381599.3 P20591-1

Frequencies

GnomAD3 genomes
AF:
0.643
AC:
97791
AN:
151984
Hom.:
33615
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.848
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.699
Gnomad ASJ
AF:
0.669
Gnomad EAS
AF:
0.993
Gnomad SAS
AF:
0.735
Gnomad FIN
AF:
0.519
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.494
Gnomad OTH
AF:
0.635
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.644
AC:
97894
AN:
152102
Hom.:
33657
Cov.:
32
AF XY:
0.648
AC XY:
48164
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.848
Gnomad4 AMR
AF:
0.699
Gnomad4 ASJ
AF:
0.669
Gnomad4 EAS
AF:
0.993
Gnomad4 SAS
AF:
0.734
Gnomad4 FIN
AF:
0.519
Gnomad4 NFE
AF:
0.494
Gnomad4 OTH
AF:
0.636
Alfa
AF:
0.563
Hom.:
3221
Bravo
AF:
0.668
Asia WGS
AF:
0.845
AC:
2937
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
1.4
DANN
Benign
0.76

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: rs455599; hg19: chr21-42804679; API