rs12484907

Variant names:

• chr22-50149884-G-A
• rs12484907
• NM_018995.3:c.2727+170G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018995.3(MOV10L1):​c.2727+170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,284 control chromosomes in the GnomAD database, including 244 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 0.043 (244 hom., cov: 33)
• Consequence: MOV10L1 NM_018995.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.2727+170G>A		intron_variant	Intron 20 of 26	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2727+170G>A		intron_variant	Intron 20 of 26	1	NM_018995.3	ENSP00000262794.5

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6482 AN: 152164 Hom.: 241 Cov.: 33

Gnomad AFR AF: 0.00862

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0492

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0426 AC: 6488 AN: 152284 Hom.: 244 Cov.: 33 AF XY: 0.0465 AC XY: 3465 AN XY: 74454

African (AFR) AF: 0.00857 AC: 356 AN: 41560

American (AMR) AF: 0.0888 AC: 1358 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3472

East Asian (EAS) AF: 0.109 AC: 564 AN: 5188

South Asian (SAS) AF: 0.155 AC: 748 AN: 4818

European-Finnish (FIN) AF: 0.0608 AC: 646 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2623 AN: 68018

Other (OTH) AF: 0.0487 AC: 103 AN: 2116

Alfa AF: 0.0477 Hom.: 521

Bravo AF: 0.0448

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		0.13
PromoterAI		0.00080	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12484907; hg19: chr22-50588313;