chr1-112673921-A-G

Variant names:

• chr1-112673921-A-G
• rs2932538
• ENST00000486416.1:n.311+470A>G

Variant summary

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

The ENST00000486416.1(MOV10):​n.311+470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,172 control chromosomes in the GnomAD database, including 47,061 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 0.78 (47061 hom., cov: 32)
• Consequence: MOV10 ENST00000486416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 80 publications found

Genes affected

MOV10 (HGNC:7200): (Mov10 RNA helicase) Enables 5'-3' RNA helicase activity and RNA binding activity. Involved in defense response to virus; negative regulation of transposition, RNA-mediated; and posttranscriptional regulation of gene expression. Located in P-body and cytosol. Implicated in hypertension. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10	ENST00000486416.1	n.311+470A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119266 AN: 152054 Hom.: 47011 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.784 AC: 119371 AN: 152172 Hom.: 47061 Cov.: 32 AF XY: 0.790 AC XY: 58766 AN XY: 74404

African (AFR) AF: 0.822 AC: 34129 AN: 41510

American (AMR) AF: 0.845 AC: 12917 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2726 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4233 AN: 5182

South Asian (SAS) AF: 0.876 AC: 4229 AN: 4828

European-Finnish (FIN) AF: 0.776 AC: 8218 AN: 10592

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.740 AC: 50331 AN: 67984

Other (OTH) AF: 0.798 AC: 1686 AN: 2112

Alfa AF: 0.755 Hom.: 138373

Bravo AF: 0.793

Asia WGS AF: 0.857 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		1.5
PromoterAI		-0.0013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2932538; hg19: chr1-113216543; COSMIC: COSV54144805;