rs2272836

Variant names:

• chr22-50144121-C-A
• rs2272836
• NM_018995.3:c.2383C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50144121-C-A
• chr22-50144121-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018995.3(MOV10L1):​c.2383C>A​(p.Arg795Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.19 in 1,609,978 control chromosomes in the GnomAD database, including 31,538 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 0.19 (3019 hom., cov: 33)
  • Exomes 𝑓: 0.19 (28519 hom.)
• Consequence: MOV10L1 NM_018995.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.55
• Publications: 22 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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.2383C>A	p.Arg795Arg	synonymous	Exon 18 of 27	NP_061868.1	Q9BXT6-1
	MOV10L1	NM_001164104.2		c.2383C>A	p.Arg795Arg	synonymous	Exon 18 of 26	NP_001157576.1	Q9BXT6-4
	MOV10L1	NM_001164105.2		c.2323C>A	p.Arg775Arg	synonymous	Exon 18 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.2383C>A	p.Arg795Arg	synonymous	Exon 18 of 27	ENSP00000262794.5	Q9BXT6-1
	MOV10L1	ENST00000395858.7	TSL:1	c.2383C>A	p.Arg795Arg	synonymous	Exon 18 of 26	ENSP00000379199.3	Q9BXT6-4
	MOV10L1	ENST00000540615.5	TSL:2	c.2323C>A	p.Arg775Arg	synonymous	Exon 18 of 26	ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28754 AN: 152106 Hom.: 3001 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.206

GnomAD2 exomes AF: 0.233 AC: 58453 AN: 251206 AF XY: 0.229

Gnomad AFR exome AF: 0.157

Gnomad AMR exome AF: 0.416

Gnomad ASJ exome AF: 0.221

Gnomad EAS exome AF: 0.263

Gnomad FIN exome AF: 0.177

Gnomad NFE exome AF: 0.179

Gnomad OTH exome AF: 0.219

GnomAD4 exome AF: 0.190 AC: 276586 AN: 1457754 Hom.: 28519 Cov.: 32 AF XY: 0.192 AC XY: 139313 AN XY: 724388

African (AFR) AF: 0.160 AC: 5332 AN: 33422

American (AMR) AF: 0.407 AC: 18194 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 5628 AN: 26080

East Asian (EAS) AF: 0.264 AC: 10463 AN: 39566

South Asian (SAS) AF: 0.291 AC: 25045 AN: 86102

European-Finnish (FIN) AF: 0.177 AC: 9426 AN: 53378

Middle Eastern (MID) AF: 0.185 AC: 1063 AN: 5748

European-Non Finnish (NFE) AF: 0.171 AC: 189671 AN: 1108614

Other (OTH) AF: 0.195 AC: 11764 AN: 60180

GnomAD4 genome AF: 0.189 AC: 28804 AN: 152224 Hom.: 3019 Cov.: 33 AF XY: 0.191 AC XY: 14216 AN XY: 74428

African (AFR) AF: 0.154 AC: 6395 AN: 41536

American (AMR) AF: 0.309 AC: 4729 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1322 AN: 5176

South Asian (SAS) AF: 0.289 AC: 1396 AN: 4830

European-Finnish (FIN) AF: 0.160 AC: 1696 AN: 10596

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11776 AN: 68008

Other (OTH) AF: 0.215 AC: 454 AN: 2116

Alfa AF: 0.178 Hom.: 4014

Bravo AF: 0.201

Asia WGS AF: 0.285 AC: 988 AN: 3478

EpiCase AF: 0.165

EpiControl AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.88
PhyloP100		4.6
Mutation Taster		=183/117	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.30		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.30		Position offset: 29

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

Other links and lift over

dbSNP: rs2272836; hg19: chr22-50582550; COSMIC: COSV53168312; COSMIC: COSV53168312;