rs2272840

chr22-50149724-G-Achr22-50149724-G-Cchr22-50149724-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018995.3(MOV10L1):c.2727+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,608,630 control chromosomes in the GnomAD database, including 50,022 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 (4350 hom., cov: 32)
  • Exomes 𝑓: 0.25 (45672 hom.)
• Consequence: MOV10L1 NM_018995.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOV10L1	NM_018995.3	c.2727+10G>A		intron_variant		ENST00000262794.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2727+10G>A		intron_variant		1	NM_018995.3	P1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34758 AN: 151988 Hom.: 4335 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.272

GnomAD3 exomes AF: 0.271 AC: 66337 AN: 245022 Hom.: 9535 AF XY: 0.272 AC XY: 35992 AN XY: 132526

Gnomad AFR exome AF: 0.161

Gnomad AMR exome AF: 0.409

Gnomad ASJ exome AF: 0.254

Gnomad EAS exome AF: 0.273

Gnomad SAS exome AF: 0.327

Gnomad FIN exome AF: 0.208

Gnomad NFE exome AF: 0.241

Gnomad OTH exome AF: 0.276

GnomAD4 exome AF: 0.247 AC: 359802 AN: 1456524 Hom.: 45672 Cov.: 32 AF XY: 0.249 AC XY: 180674 AN XY: 724446

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.409

Gnomad4 ASJ exome AF: 0.248

Gnomad4 EAS exome AF: 0.281

Gnomad4 SAS exome AF: 0.323

Gnomad4 FIN exome AF: 0.209

Gnomad4 NFE exome AF: 0.238

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.229 AC: 34802 AN: 152106 Hom.: 4350 Cov.: 32 AF XY: 0.230 AC XY: 17133 AN XY: 74380

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.279

Alfa AF: 0.224 Hom.: 1202

Bravo AF: 0.239

Asia WGS AF: 0.307 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.1
Dann	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs2272840; hg19: chr22-50588153; COSMIC: COSV53168808;