21-41460237-G-A

Variant names:

• chr21-41460237-G-A
• rs8127290
• ENST00000679386.1:c.1758+7368G>A

Variant summary

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

The ENST00000679386.1(MX1):​c.1758+7368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,016 control chromosomes in the GnomAD database, including 4,371 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 0.22 (4371 hom., cov: 32)
• Consequence: MX1 ENST00000679386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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.1758+7368G>A		intron	N/A	ENSP00000505700.1	A0A7P0T9R0

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33391 AN: 151898 Hom.: 4360 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.220 AC: 33445 AN: 152016 Hom.: 4371 Cov.: 32 AF XY: 0.224 AC XY: 16650 AN XY: 74304

African (AFR) AF: 0.345 AC: 14267 AN: 41412

American (AMR) AF: 0.128 AC: 1959 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5166

South Asian (SAS) AF: 0.223 AC: 1072 AN: 4816

European-Finnish (FIN) AF: 0.265 AC: 2801 AN: 10566

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10898 AN: 67974

Other (OTH) AF: 0.178 AC: 376 AN: 2116

Alfa AF: 0.179 Hom.: 1371

Bravo AF: 0.214

Asia WGS AF: 0.303 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.73
PhyloP100		-1.2

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: rs8127290;

hg19: chr21-42832164;