dbSNP rs17000900: MX1:c.-294C>A (chr21-41426103-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000455164.6(MX1):c.-294C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 173,842 control chromosomes in the GnomAD database, including 1,764 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 0.14 ( 1671 hom., cov: 33)

Exomes 𝑓: 0.089 ( 93 hom. )

Consequence

MX1
ENST00000455164.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138

Publications

29 publications found

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]

MX1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MX1	NM_002462.5 link	c.-469C>A		upstream_gene_variant		ENST00000398598.8	NP_002453.2	P20591-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MX1	ENST00000398598.8 link	c.-469C>A		upstream_gene_variant		1	NM_002462.5	ENSP00000381599.3		P20591-1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20871

AN:

152184

Hom.:

1672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.0820

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.121

GnomAD4 exome

AF:

0.0889

AC:

1914

AN:

21540

Hom.:

Cov.:

AF XY:

0.0882

AC XY:

1002

AN XY:

11360

show subpopulations

African (AFR)

AF:

0.151

AC:

AN:

530

American (AMR)

AF:

0.0977

AC:

AN:

440

Ashkenazi Jewish (ASJ)

AF:

0.0598

AC:

AN:

602

East Asian (EAS)

AF:

0.149

AC:

342

AN:

2300

South Asian (SAS)

AF:

0.193

AC:

AN:

150

European-Finnish (FIN)

AF:

0.0741

AC:

194

AN:

2618

Middle Eastern (MID)

AF:

0.105

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0797

AC:

1086

AN:

13620

Other (OTH)

AF:

0.0796

AC:

AN:

1194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

173

259

346

432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.137

AC:

20889

AN:

152302

Hom.:

1671

Cov.:

AF XY:

0.135

AC XY:

10067

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.206

AC:

8548

AN:

41550

American (AMR)

AF:

0.109

AC:

1669

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0838

AC:

291

AN:

3472

East Asian (EAS)

AF:

0.149

AC:

772

AN:

5180

South Asian (SAS)

AF:

0.228

AC:

1100

AN:

4824

European-Finnish (FIN)

AF:

0.0820

AC:

871

AN:

10622

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7194

AN:

68032

Other (OTH)

AF:

0.121

AC:

255

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

916

1831

2747

3662

4578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.116

Hom.:

381

Bravo

AF:

0.141

Asia WGS

AF:

0.159

AC:

555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.7

(source)

DANN

Benign

0.59

PhyloP100

-0.14

PromoterAI

0.27

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over