Genetic Variant MX1:c.-982C>G (chr21-41420558-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001144925.2(MX1):c.-982C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,148 control chromosomes in the GnomAD database, including 10,591 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 0.35 ( 10587 hom., cov: 33)

Exomes 𝑓: 0.36 ( 4 hom. )

Consequence

MX1
NM_001144925.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510

Publications

10 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:

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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=-1.06).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144925.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MX1	NM_001144925.2		c.-982C>G		5_prime_UTR	Exon 1 of 19	NP_001138397.1	P20591-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MX1	ENST00000398600.6	TSL:2	c.-982C>G	5_prime_UTR	Exon 1 of 19	ENSP00000381601.2	P20591-1
MX1	ENST00000896027.1		c.-1040C>G	5_prime_UTR	Exon 1 of 19	ENSP00000566086.1
MX1	ENST00000967463.1		c.-896C>G	5_prime_UTR	Exon 1 of 19	ENSP00000637522.1

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53551

AN:

151954

Hom.:

10588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.576

Gnomad SAS

AF:

0.362

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.376

GnomAD4 exome

AF:

0.355

AC:

AN:

Hom.:

Cov.:

AF XY:

0.440

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.357

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

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:

0.352

AC:

53566

AN:

152072

Hom.:

10587

Cov.:

AF XY:

0.357

AC XY:

26548

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.164

AC:

6797

AN:

41488

American (AMR)

AF:

0.439

AC:

6720

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

1696

AN:

3468

East Asian (EAS)

AF:

0.577

AC:

2974

AN:

5158

South Asian (SAS)

AF:

0.362

AC:

1746

AN:

4818

European-Finnish (FIN)

AF:

0.442

AC:

4669

AN:

10558

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.408

AC:

27727

AN:

67966

Other (OTH)

AF:

0.377

AC:

797

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1730

3460

5190

6920

8650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.366

Hom.:

1400

Bravo

AF:

0.347

Asia WGS

AF:

0.471

AC:

1632

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

6.8

(source)

DANN

Benign

0.61

PhyloP100

0.051

PromoterAI

-0.23

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over