Genetic Variant MYEOV:n.329A>G (chr11-69294492-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000535653.1(MYEOV):n.329A>G variant causes a non coding transcript exon 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
ENST00000535653.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

10 publications found

Variant links:

Genes affected

MYEOV (HGNC:7563): (myeloma overexpressed)

MYEOV links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYEOV	NM_001293291.2 link	c.-207A>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000441339.3	NP_001280220.1	Q96EZ4A0A024R5F1A8K256

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYEOV	ENST00000441339.3 link	c.-207A>G		5_prime_UTR_variant	Exon 1 of 3	2	NM_001293291.2	ENSP00000412482.2		Q96EZ4

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49445

AN:

151632

Hom.:

11373

Cov.:

show subpopulations

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:

AN:

252

Hom.:

Cov.:

AF XY:

0.301

AC XY:

AN XY:

186

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.143

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.282

AC:

AN:

188

Other (OTH)

AF:

0.545

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.326

AC:

49525

AN:

151750

Hom.:

11400

Cov.:

AF XY:

0.329

AC XY:

24380

AN XY:

74108

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.174

AC:

11843

AN:

67916

Other (OTH)

AF:

0.293

AC:

616

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1364

2728

4091

5455

6819

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.52

(source)

DANN

Benign

0.28

PhyloP100

-1.5

PromoterAI

-0.014

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over