Genetic Variant BMERB1:c.*1336G>A (chr16-15588165-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_033201.3(BMERB1):c.*1336G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,048 control chromosomes in the GnomAD database, including 40,511 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 0.72 ( 40507 hom., cov: 32)

Exomes 𝑓: 0.90 ( 4 hom. )

Consequence

BMERB1
NM_033201.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.845

Publications

1 publications found

Variant links:

Genes affected

BMERB1 (HGNC:19213): (bMERB domain containing 1) Predicted to act upstream of or within negative regulation of cell motility involved in cerebral cortex radial glia guided migration and negative regulation of microtubule depolymerization. Predicted to be located in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

BMERB1 links:

MPV17L-BMERB1 (HGNC:):

MPV17L-BMERB1 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033201.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BMERB1	NM_033201.3	MANE Select	c.*1336G>A	3_prime_UTR	Exon 6 of 6	NP_149978.1	Q96MC5-1
MPV17L-BMERB1	NM_001414674.1		c.*1336G>A	3_prime_UTR	Exon 6 of 6	NP_001401603.1
BMERB1	NM_001142469.2		c.*1336G>A	3_prime_UTR	Exon 6 of 6	NP_001135941.1	Q96MC5-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BMERB1	ENST00000300006.9	TSL:1 MANE Select	c.*1336G>A	3_prime_UTR	Exon 6 of 6	ENSP00000300006.4	Q96MC5-1
BMERB1	ENST00000962100.1		c.*1336G>A	3_prime_UTR	Exon 6 of 6	ENSP00000632159.1
BMERB1	ENST00000565857.1	TSL:4	c.272-2865G>A	intron	N/A	ENSP00000456084.1	H3BR56

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109754

AN:

151920

Hom.:

40451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.892

Gnomad AMI

AF:

0.718

Gnomad AMR

AF:

0.700

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.753

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.710

GnomAD4 exome

AF:

0.900

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.723

AC:

109870

AN:

152038

Hom.:

40507

Cov.:

AF XY:

0.724

AC XY:

53794

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.892

AC:

37010

AN:

41488

American (AMR)

AF:

0.701

AC:

10707

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2505

AN:

3468

East Asian (EAS)

AF:

0.632

AC:

3266

AN:

5168

South Asian (SAS)

AF:

0.753

AC:

3627

AN:

4814

European-Finnish (FIN)

AF:

0.670

AC:

7073

AN:

10558

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43318

AN:

67948

Other (OTH)

AF:

0.709

AC:

1497

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1503

3006

4509

6012

7515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<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:

0.654

Hom.:

13097

Bravo

AF:

0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.36

(source)

DANN

Benign

0.66

PhyloP100

-0.84

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over