rs2272838

Variant names:

• chr22-50145772-A-C
• rs2272838
• NM_018995.3:c.2589A>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_018995.3(MOV10L1):​c.2589A>C​(p.Thr863Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,613,754 control chromosomes in the GnomAD database, including 50,202 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 0.23 (4319 hom., cov: 32)
  • Exomes 𝑓: 0.25 (45883 hom.)
• Consequence: MOV10L1 NM_018995.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 18 publications found

Genes affected

MOV10L1 (HGNC:7201): (Mov10 like RNA helicase 1) This gene is similar to a mouse gene that encodes a putative RNA helicase and shows testis-specific expression. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP7: Synonymous conserved (PhyloP=-2.72 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018995.3. 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
	MOV10L1	NM_018995.3	MANE Select	c.2589A>C	p.Thr863Thr	synonymous	Exon 19 of 27	NP_061868.1	Q9BXT6-1
	MOV10L1	NM_001164104.2		c.2589A>C	p.Thr863Thr	synonymous	Exon 19 of 26	NP_001157576.1	Q9BXT6-4
	MOV10L1	NM_001164105.2		c.2529A>C	p.Thr843Thr	synonymous	Exon 19 of 26	NP_001157577.1	Q9BXT6-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10L1	ENST00000262794.10	TSL:1 MANE Select	c.2589A>C	p.Thr863Thr	synonymous	Exon 19 of 27	ENSP00000262794.5	Q9BXT6-1
	MOV10L1	ENST00000395858.7	TSL:1	c.2589A>C	p.Thr863Thr	synonymous	Exon 19 of 26	ENSP00000379199.3	Q9BXT6-4
	MOV10L1	ENST00000540615.5	TSL:2	c.2529A>C	p.Thr843Thr	synonymous	Exon 19 of 26	ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34577 AN: 152018 Hom.: 4304 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.269

GnomAD2 exomes AF: 0.269 AC: 67691 AN: 251378 AF XY: 0.270

Gnomad AFR exome AF: 0.157

Gnomad AMR exome AF: 0.413

Gnomad ASJ exome AF: 0.252

Gnomad EAS exome AF: 0.278

Gnomad FIN exome AF: 0.201

Gnomad NFE exome AF: 0.240

Gnomad OTH exome AF: 0.273

GnomAD4 exome AF: 0.247 AC: 360747 AN: 1461616 Hom.: 45883 Cov.: 34 AF XY: 0.249 AC XY: 181094 AN XY: 727102

African (AFR) AF: 0.160 AC: 5362 AN: 33476

American (AMR) AF: 0.411 AC: 18385 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 6433 AN: 26136

East Asian (EAS) AF: 0.283 AC: 11251 AN: 39696

South Asian (SAS) AF: 0.320 AC: 27578 AN: 86254

European-Finnish (FIN) AF: 0.202 AC: 10786 AN: 53324

Middle Eastern (MID) AF: 0.256 AC: 1473 AN: 5746

European-Non Finnish (NFE) AF: 0.238 AC: 264442 AN: 1111882

Other (OTH) AF: 0.249 AC: 15037 AN: 60384

GnomAD4 genome AF: 0.228 AC: 34621 AN: 152138 Hom.: 4319 Cov.: 32 AF XY: 0.229 AC XY: 16995 AN XY: 74376

African (AFR) AF: 0.157 AC: 6509 AN: 41494

American (AMR) AF: 0.354 AC: 5409 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1399 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1532 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 1996 AN: 10582

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16011 AN: 67996

Other (OTH) AF: 0.276 AC: 584 AN: 2114

Alfa AF: 0.239 Hom.: 7208

Bravo AF: 0.239

Asia WGS AF: 0.304 AC: 1057 AN: 3478

EpiCase AF: 0.231

EpiControl AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.28
PhyloP100		-2.7
Mutation Taster		=283/17	polymorphism (auto)

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: rs2272838; hg19: chr22-50584201; COSMIC: COSV53168149; COSMIC: COSV53168149;