rs738490

chr22-50092222-G-Achr22-50092222-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.282+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,575,500 control chromosomes in the GnomAD database, including 25,021 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 0.14 (1946 hom., cov: 32)
  • Exomes 𝑓: 0.18 (23075 hom.)
• Consequence: MOV10L1 NM_018995.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOV10L1	NM_018995.3	c.282+37G>A		intron_variant		ENST00000262794.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOV10L1	ENST00000262794.10	c.282+37G>A		intron_variant		1	NM_018995.3	P1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22017 AN: 152026 Hom.: 1946 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.159

GnomAD3 exomes AF: 0.185 AC: 43496 AN: 235186 Hom.: 4247 AF XY: 0.190 AC XY: 24107 AN XY: 126654

Gnomad AFR exome AF: 0.0404

Gnomad AMR exome AF: 0.157

Gnomad ASJ exome AF: 0.223

Gnomad EAS exome AF: 0.268

Gnomad SAS exome AF: 0.235

Gnomad FIN exome AF: 0.223

Gnomad NFE exome AF: 0.178

Gnomad OTH exome AF: 0.188

GnomAD4 exome AF: 0.176 AC: 250290 AN: 1423356 Hom.: 23075 Cov.: 26 AF XY: 0.178 AC XY: 125771 AN XY: 706810

Gnomad4 AFR exome AF: 0.0428

Gnomad4 AMR exome AF: 0.153

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.319

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.145 AC: 22022 AN: 152144 Hom.: 1946 Cov.: 32 AF XY: 0.149 AC XY: 11106 AN XY: 74374

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.158

Alfa AF: 0.148 Hom.: 983

Bravo AF: 0.134

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.58
Dann	Benign	0.67

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: rs738490; hg19: chr22-50530651; COSMIC: COSV53170438; COSMIC: COSV53170438;