22-50092159-G-T

Variant names:

• chr22-50092159-G-T
• rs540038775
• NM_018995.3:c.256G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_018995.3(MOV10L1):​c.256G>T​(p.Val86Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V86M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MOV10L1 NM_018995.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16044888).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.256G>T	p.Val86Leu	missense_variant	Exon 2 of 27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.256G>T	p.Val86Leu	missense_variant	Exon 2 of 27	1	NM_018995.3	ENSP00000262794.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.060	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.97
DEOGEN2	Benign	0.072	T;T;.;.
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.30
FATHMM_MKL	Benign	0.37	N
LIST_S2	Benign	0.81	T;.;T;T
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Benign	-0.60	T
MutationAssessor	Uncertain	2.2	M;M;M;.
PhyloP100		3.6
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Benign	0.13
Sift	Benign	0.32	T;T;T;T
Sift4G	Benign	0.36	T;T;T;T
Polyphen		0.10	B;B;.;.
Vest4		0.27
MutPred		0.45		Loss of methylation at K85 (P = 0.0438);Loss of methylation at K85 (P = 0.0438);Loss of methylation at K85 (P = 0.0438);.;
MVP		0.77
MPC		0.10
ClinPred		0.54	D
GERP RS		2.9
Varity_R		0.045
gMVP		0.31
Mutation Taster		=284/16	polymorphism

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: rs540038775; hg19: chr22-50530588;