1-112673921-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486416.1(MOV10):n.311+470A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10	ENST00000486416.1	n.311+470A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.798

Alfa AF: 0.755 Hom.: 48750

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

Splicing

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

Publications

LitVar

Other links and lift over

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