chr22-50144121-C-A

Position:

• chr22-50144121-C-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018995.3(MOV10L1):​c.2383C>A​(p.Arg795=) 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

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOV10L1	NM_018995.3	c.2383C>A	p.Arg795=	synonymous_variant	18/27	ENST00000262794.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2383C>A	p.Arg795=	synonymous_variant	18/27	1	NM_018995.3	P1
MOV10L1	ENST00000395858.7	c.2383C>A	p.Arg795=	synonymous_variant	18/26	1
MOV10L1	ENST00000540615.5	c.2323C>A	p.Arg775=	synonymous_variant	18/26	2

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

GnomAD3 exomes AF: 0.233 AC: 58453 AN: 251206 Hom.: 7893 AF XY: 0.229 AC XY: 31073 AN XY: 135760

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 SAS exome AF: 0.294

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

Gnomad4 AFR exome AF: 0.160

Gnomad4 AMR exome AF: 0.407

Gnomad4 ASJ exome AF: 0.216

Gnomad4 EAS exome AF: 0.264

Gnomad4 SAS exome AF: 0.291

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.171

Gnomad4 OTH exome AF: 0.195

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.215

Alfa AF: 0.177 Hom.: 3446

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

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