chr1-112689067-G-A

Variant names:

• chr1-112689067-G-A
• rs200320463
• NM_001321324.2:c.270G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001321324.2(MOV10):​c.270G>A​(p.Lys90Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MOV10 NM_001321324.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 1 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP7: Synonymous conserved (PhyloP=0.382 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321324.2. 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
	MOV10	NM_001321324.2	MANE Select	c.270G>A	p.Lys90Lys	synonymous	Exon 3 of 21	NP_001308253.1	Q9HCE1-1
	MOV10	NM_001130079.3		c.270G>A	p.Lys90Lys	synonymous	Exon 3 of 21	NP_001123551.1	Q9HCE1-1
	MOV10	NM_001369507.1		c.270G>A	p.Lys90Lys	synonymous	Exon 2 of 20	NP_001356436.1	Q9HCE1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10	ENST00000369645.6	TSL:5 MANE Select	c.270G>A	p.Lys90Lys	synonymous	Exon 3 of 21	ENSP00000358659.1	Q9HCE1-1
	MOV10	ENST00000357443.2	TSL:1	c.270G>A	p.Lys90Lys	synonymous	Exon 2 of 20	ENSP00000350028.2	Q9HCE1-1
	MOV10	ENST00000413052.6	TSL:1	c.270G>A	p.Lys90Lys	synonymous	Exon 3 of 21	ENSP00000399797.2	Q9HCE1-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	7.8
DANN	Benign	0.91
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs200320463; hg19: chr1-113231689;