rs138271

Variant names:

• chr22-50149702-C-A
• rs138271
• NM_018995.3:c.2715C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50149702-C-A
• chr22-50149702-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018995.3(MOV10L1):​c.2715C>A​(p.Asp905Glu) 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MOV10L1 NM_018995.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.036733598).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018995.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10L1	NM_018995.3	MANE Select	c.2715C>A	p.Asp905Glu	missense	Exon 20 of 27	NP_061868.1	Q9BXT6-1
	MOV10L1	NM_001164104.2		c.2715C>A	p.Asp905Glu	missense	Exon 20 of 26	NP_001157576.1	Q9BXT6-4
	MOV10L1	NM_001164105.2		c.2655C>A	p.Asp885Glu	missense	Exon 20 of 26	NP_001157577.1	Q9BXT6-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10L1	ENST00000262794.10	TSL:1 MANE Select	c.2715C>A	p.Asp905Glu	missense	Exon 20 of 27	ENSP00000262794.5	Q9BXT6-1
	MOV10L1	ENST00000395858.7	TSL:1	c.2715C>A	p.Asp905Glu	missense	Exon 20 of 26	ENSP00000379199.3	Q9BXT6-4
	MOV10L1	ENST00000540615.5	TSL:2	c.2655C>A	p.Asp885Glu	missense	Exon 20 of 26	ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.073	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	0.060
DANN	Benign	0.17
DEOGEN2	Benign	0.13	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.099	N
LIST_S2	Benign	0.73	T
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.037	T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	-1.1	N
PhyloP100		0.34
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.16
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0010	B
Vest4		0.065
MutPred		0.41		Gain of sheet (P = 0.039)
MVP		0.51
MPC		0.55
ClinPred		0.036	T
GERP RS		-4.9
PromoterAI		-0.021	Neutral
Varity_R		0.071
gMVP		0.29
Mutation Taster		=94/6	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs138271; hg19: chr22-50588131;