chr22-50144201-G-A

Position:

• chr22-50144201-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_018995.3(MOV10L1):​c.2463G>A​(p.Pro821=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 1,610,790 control chromosomes in the GnomAD database, including 3,372 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 0.045 (211 hom., cov: 33)
  • Exomes 𝑓: 0.061 (3161 hom.)
• Consequence: MOV10L1 NM_018995.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94

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=-0.84).
• BP7: Synonymous conserved (PhyloP=-3.94 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOV10L1	NM_018995.3	c.2463G>A	p.Pro821=	synonymous_variant	18/27	ENST00000262794.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2463G>A	p.Pro821=	synonymous_variant	18/27	1	NM_018995.3	P1
MOV10L1	ENST00000395858.7	c.2463G>A	p.Pro821=	synonymous_variant	18/26	1
MOV10L1	ENST00000540615.5	c.2403G>A	p.Pro801=	synonymous_variant	18/26	2

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6805 AN: 152200 Hom.: 211 Cov.: 33

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0607

GnomAD3 exomes AF: 0.0496 AC: 12454 AN: 251076 Hom.: 459 AF XY: 0.0520 AC XY: 7052 AN XY: 135744

Gnomad AFR exome AF: 0.00978

Gnomad AMR exome AF: 0.0282

Gnomad ASJ exome AF: 0.154

Gnomad EAS exome AF: 0.000163

Gnomad SAS exome AF: 0.0303

Gnomad FIN exome AF: 0.0356

Gnomad NFE exome AF: 0.0673

Gnomad OTH exome AF: 0.0695

GnomAD4 exome AF: 0.0610 AC: 88910 AN: 1458472 Hom.: 3161 Cov.: 32 AF XY: 0.0609 AC XY: 44152 AN XY: 724954

Gnomad4 AFR exome AF: 0.0108

Gnomad4 AMR exome AF: 0.0310

Gnomad4 ASJ exome AF: 0.149

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.0312

Gnomad4 FIN exome AF: 0.0344

Gnomad4 NFE exome AF: 0.0668

Gnomad4 OTH exome AF: 0.0642

GnomAD4 genome AF: 0.0447 AC: 6803 AN: 152318 Hom.: 211 Cov.: 33 AF XY: 0.0426 AC XY: 3170 AN XY: 74484

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0367

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0276

Gnomad4 FIN AF: 0.0327

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0671 Hom.: 218

Bravo AF: 0.0449

Asia WGS AF: 0.0160 AC: 55 AN: 3478

EpiCase AF: 0.0732

EpiControl AF: 0.0747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.036
DANN	Benign	0.82

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: rs11704548; hg19: chr22-50582630; COSMIC: COSV53171476; COSMIC: COSV53171476;