rs7103126

Variant names:

• chr11-69295926-T-A
• rs7103126
• NM_001293291.2:c.476T>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Uncertain significance. The variant received 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. 14/21 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: 32)
• Consequence: MYEOV NM_001293291.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.29
• Publications: 31 publications found

Genes affected

MYEOV (HGNC:7563): (myeloma overexpressed)

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=0.072019964).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001293291.2. 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
	MYEOV	NM_001293291.2	MANE Select	c.476T>A	p.Val159Glu	missense	Exon 3 of 3	NP_001280220.1	Q96EZ4
	MYEOV	NM_138768.4		c.476T>A	p.Val159Glu	missense	Exon 3 of 3	NP_620123.2
	MYEOV	NM_001293294.2		c.302T>A	p.Val101Glu	missense	Exon 2 of 2	NP_001280223.1	F5H0B3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEOV	ENST00000441339.3	TSL:2 MANE Select	c.476T>A	p.Val159Glu	missense	Exon 3 of 3	ENSP00000412482.2	Q96EZ4
	MYEOV	ENST00000308946.3	TSL:1	c.476T>A	p.Val159Glu	missense	Exon 3 of 3	ENSP00000308330.3	Q96EZ4
	MYEOV	ENST00000535653.1	TSL:1	n.1107T>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.0074	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.0018	T
MetaRNN	Benign	0.072	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-4.3
PrimateAI	Benign	0.27	T
PROVEAN	Pathogenic	-4.4	D
REVEL	Benign	0.021
Polyphen		0.27	B
Vest4		0.36
MutPred		0.42		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
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7103126; hg19: chr11-69063393;