rs1557372

Variant names:

• chr21-41460614-C-T
• rs1557372
• ENST00000679386.1:c.1759-7623C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000679386.1(MX1):​c.1759-7623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,940 control chromosomes in the GnomAD database, including 12,267 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 0.40 (12267 hom., cov: 32)
• Consequence: MX1 ENST00000679386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 12 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679386.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MX1	ENST00000679386.1		c.1759-7623C>T		intron	N/A	ENSP00000505700.1	A0A7P0T9R0

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60285 AN: 151822 Hom.: 12262 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.397 AC: 60323 AN: 151940 Hom.: 12267 Cov.: 32 AF XY: 0.395 AC XY: 29342 AN XY: 74264

African (AFR) AF: 0.466 AC: 19283 AN: 41410

American (AMR) AF: 0.371 AC: 5671 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5158

South Asian (SAS) AF: 0.346 AC: 1663 AN: 4812

European-Finnish (FIN) AF: 0.381 AC: 4018 AN: 10542

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25030 AN: 67964

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.385 Hom.: 16372

Bravo AF: 0.403

Asia WGS AF: 0.362 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.48
PhyloP100		-0.065

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1557372;

hg19: chr21-42832541;