rs2272838

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 of 27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 of 27	1	NM_018995.3	ENSP00000262794.5
MOV10L1	ENST00000395858.7	c.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 of 26	1		ENSP00000379199.3
MOV10L1	ENST00000540615.5	c.2529A>C	p.Thr843Thr	synonymous_variant	Exon 19 of 26	2		ENSP00000438542.1

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

GnomAD3 exomes AF: 0.269 AC: 67691 AN: 251378 Hom.: 9913 AF XY: 0.270 AC XY: 36677 AN XY: 135870

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 SAS exome AF: 0.323

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

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.411

Gnomad4 ASJ exome AF: 0.246

Gnomad4 EAS exome AF: 0.283

Gnomad4 SAS exome AF: 0.320

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.238

Gnomad4 OTH exome AF: 0.249

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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.276

Alfa AF: 0.239 Hom.: 5790

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.28

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

Publications

LitVar

Other links and lift over

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