NM_001293291.2:c.-207A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001293291.2(MYEOV):​c.-207A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,002 control chromosomes in the GnomAD database, including 11,417 homozygotes. 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: 𝑓 0.33 (11400 hom., cov: 32)
  • Exomes 𝑓: 0.32 (17 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

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>G		5_prime_UTR	Exon 1 of 3	NP_001280220.1
	MYEOV	NM_138768.4		c.-113A>G		5_prime_UTR	Exon 1 of 3	NP_620123.2
	MYEOV	NM_001293294.2		c.-477A>G		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>G		5_prime_UTR	Exon 1 of 3	ENSP00000412482.2
	MYEOV	ENST00000308946.3	TSL:1	c.-113A>G		5_prime_UTR	Exon 1 of 3	ENSP00000308330.3
	MYEOV	ENST00000535653.1	TSL:1	n.329A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49445 AN: 151632 Hom.: 11373 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.321 AC: 81 AN: 252 Hom.: 17 Cov.: 0 AF XY: 0.301 AC XY: 56 AN XY: 186

African (AFR) AF: 0.750 AC: 6 AN: 8

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 6 AN: 12

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.143 AC: 2 AN: 14

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.282 AC: 53 AN: 188

Other (OTH) AF: 0.545 AC: 12 AN: 22

GnomAD4 genome AF: 0.326 AC: 49525 AN: 151750 Hom.: 11400 Cov.: 32 AF XY: 0.329 AC XY: 24380 AN XY: 74108

African (AFR) AF: 0.648 AC: 26800 AN: 41386

American (AMR) AF: 0.219 AC: 3336 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2159 AN: 5126

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4816

European-Finnish (FIN) AF: 0.197 AC: 2065 AN: 10494

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11843 AN: 67916

Other (OTH) AF: 0.293 AC: 616 AN: 2100

Alfa AF: 0.219 Hom.: 8398

Bravo AF: 0.335

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.28
PhyloP100		-1.5
PromoterAI		-0.014	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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;