chr1-112689610-C-T

Variant names:

• chr1-112689610-C-T
• rs74467987
• NM_001321324.2:c.537C>T

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_001321324.2(MOV10):​c.537C>T​(p.Phe179Phe) variant causes a synonymous change. The variant allele was found at a frequency of 0.00258 in 1,614,212 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0029 (16 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (151 hom.)
• Consequence: MOV10 NM_001321324.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 4.78
• Publications: 3 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 -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BP6: Variant 1-112689610-C-T is Benign according to our data. Variant chr1-112689610-C-T is described in ClinVar as Benign. ClinVar VariationId is 713189.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

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.537C>T	p.Phe179Phe	synonymous	Exon 4 of 21	NP_001308253.1	Q9HCE1-1
	MOV10	NM_001130079.3		c.537C>T	p.Phe179Phe	synonymous	Exon 4 of 21	NP_001123551.1	Q9HCE1-1
	MOV10	NM_001369507.1		c.537C>T	p.Phe179Phe	synonymous	Exon 3 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.537C>T	p.Phe179Phe	synonymous	Exon 4 of 21	ENSP00000358659.1	Q9HCE1-1
	MOV10	ENST00000357443.2	TSL:1	c.537C>T	p.Phe179Phe	synonymous	Exon 3 of 20	ENSP00000350028.2	Q9HCE1-1
	MOV10	ENST00000413052.6	TSL:1	c.537C>T	p.Phe179Phe	synonymous	Exon 4 of 21	ENSP00000399797.2	Q9HCE1-1

Frequencies

GnomAD3 genomes AF: 0.00289 AC: 440 AN: 152208 Hom.: 16 Cov.: 32

Gnomad AFR AF: 0.000410

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00621

GnomAD2 exomes AF: 0.00535 AC: 1346 AN: 251468 AF XY: 0.00512

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.000893

Gnomad EAS exome AF: 0.0677

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000132

Gnomad OTH exome AF: 0.00244

GnomAD4 exome AF: 0.00255 AC: 3723 AN: 1461886 Hom.: 151 Cov.: 34 AF XY: 0.00248 AC XY: 1806 AN XY: 727244

African (AFR) AF: 0.0000597 AC: 2 AN: 33480

American (AMR) AF: 0.000112 AC: 5 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00103 AC: 27 AN: 26136

East Asian (EAS) AF: 0.0804 AC: 3190 AN: 39698

South Asian (SAS) AF: 0.00158 AC: 136 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.000173 AC: 1 AN: 5768

European-Non Finnish (NFE) AF: 0.0000899 AC: 100 AN: 1112008

Other (OTH) AF: 0.00434 AC: 262 AN: 60394

GnomAD4 genome AF: 0.00287 AC: 437 AN: 152326 Hom.: 16 Cov.: 32 AF XY: 0.00348 AC XY: 259 AN XY: 74480

African (AFR) AF: 0.000409 AC: 17 AN: 41574

American (AMR) AF: 0.000523 AC: 8 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.0727 AC: 376 AN: 5170

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 68032

Other (OTH) AF: 0.00567 AC: 12 AN: 2116

Alfa AF: 0.000514 Hom.: 1

Bravo AF: 0.00311

Asia WGS AF: 0.0260 AC: 91 AN: 3478

EpiCase AF: 0.000218

EpiControl AF: 0.000296

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		4.8
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs74467987; hg19: chr1-113232232; COSMIC: COSV100659424; COSMIC: COSV100659424;