rs12170772

chr22-50145832-C-Achr22-50145832-C-T

Variant summary

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

The NM_018995.3(MOV10L1):c.2627+22C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 1,612,350 control chromosomes in the GnomAD database, including 2,205 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 0.056 (303 hom., cov: 32)
  • Exomes 𝑓: 0.049 (1902 hom.)
• Consequence: MOV10L1 NM_018995.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOV10L1	NM_018995.3	c.2627+22C>A		intron_variant		ENST00000262794.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2627+22C>A		intron_variant		1	NM_018995.3	P1
MOV10L1	ENST00000395858.7	c.2627+22C>A		intron_variant		1
MOV10L1	ENST00000540615.5	c.2567+22C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8540 AN: 152168 Hom.: 302 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0610

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0478

GnomAD3 exomes AF: 0.0442 AC: 11066 AN: 250416 Hom.: 292 AF XY: 0.0449 AC XY: 6083 AN XY: 135402

Gnomad AFR exome AF: 0.0909

Gnomad AMR exome AF: 0.0172

Gnomad ASJ exome AF: 0.0187

Gnomad EAS exome AF: 0.0160

Gnomad SAS exome AF: 0.0549

Gnomad FIN exome AF: 0.0529

Gnomad NFE exome AF: 0.0481

Gnomad OTH exome AF: 0.0421

GnomAD4 exome AF: 0.0492 AC: 71879 AN: 1460066 Hom.: 1902 Cov.: 32 AF XY: 0.0493 AC XY: 35801 AN XY: 726330

Gnomad4 AFR exome AF: 0.0904

Gnomad4 AMR exome AF: 0.0182

Gnomad4 ASJ exome AF: 0.0188

Gnomad4 EAS exome AF: 0.0126

Gnomad4 SAS exome AF: 0.0554

Gnomad4 FIN exome AF: 0.0538

Gnomad4 NFE exome AF: 0.0508

Gnomad4 OTH exome AF: 0.0460

GnomAD4 genome AF: 0.0562 AC: 8552 AN: 152284 Hom.: 303 Cov.: 32 AF XY: 0.0549 AC XY: 4087 AN XY: 74466

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0268 Hom.: 18

Bravo AF: 0.0547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.17
Dann	Benign	0.55

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: rs12170772; hg19: chr22-50584261;