11-69294492-A-T

Variant names:

• chr11-69294492-A-T
• rs11228608
• NM_001293291.2:c.-207A>T

Variant summary

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

The NM_001293291.2(MYEOV):​c.-207A>T variant causes a 5 prime UTR 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. 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 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 10 publications found

Genes affected

MYEOV (HGNC:7563): (myeloma overexpressed)

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 (BayesDel_noAF=-0.92).

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.-207A>T		5_prime_UTR	Exon 1 of 3	NP_001280220.1
	MYEOV	NM_138768.4		c.-113A>T		5_prime_UTR	Exon 1 of 3	NP_620123.2
	MYEOV	NM_001293294.2		c.-477A>T		5_prime_UTR	Exon 1 of 2	NP_001280223.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEOV	ENST00000441339.3	TSL:2 MANE Select	c.-207A>T		5_prime_UTR	Exon 1 of 3	ENSP00000412482.2
	MYEOV	ENST00000308946.3	TSL:1	c.-113A>T		5_prime_UTR	Exon 1 of 3	ENSP00000308330.3
	MYEOV	ENST00000535653.1	TSL:1	n.329A>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-1.5
PromoterAI		-0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11228608; hg19: chr11-69061959;