rs7103126

Positions:

• chr11-69295926-T-A
• chr11-69295926-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001293291.2(MYEOV):​c.476T>A​(p.Val159Glu) 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. 13/20 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. V159A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYEOV NM_001293291.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.29

Genes affected

MYEOV (HGNC:7563): (myeloma overexpressed)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.072019964).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYEOV	NM_001293291.2	c.476T>A	p.Val159Glu	missense_variant	3/3	ENST00000441339.3	NP_001280220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYEOV	ENST00000441339.3	c.476T>A	p.Val159Glu	missense_variant	3/3	2	NM_001293291.2	ENSP00000412482	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.2
DANN	Benign	0.47
DEOGEN2	Benign	0.017	T;T;.
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.0074	N
LIST_S2	Benign	0.22	.;T;T
M_CAP	Benign	0.0018	T
MetaRNN	Benign	0.072	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N;N;.
MutationTaster	Benign	1.0	P;P;P
PrimateAI	Benign	0.27	T
PROVEAN	Pathogenic	-4.4	D;D;D
REVEL	Benign	0.021
Polyphen		0.27	B;B;.
Vest4		0.36
MutPred		0.42		Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);.;
MVP		0.030
MPC		0.11
ClinPred		0.10	T
GERP RS		-1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.53
gMVP		0.092

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7103126; hg19: chr11-69063393;