rs1127293

Positions:

• chr16-15588165-G-A
• chr16-15588165-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845

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]

MPV17L-BMERB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMERB1	NM_033201.3	c.*1336G>A		3_prime_UTR_variant	6/6	ENST00000300006.9	NP_149978.1
MPV17L-BMERB1	NM_001414674.1	c.*1336G>A		3_prime_UTR_variant	6/6		NP_001401603.1
BMERB1	NM_001142469.2	c.*1336G>A		3_prime_UTR_variant	6/6		NP_001135941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMERB1	ENST00000300006.9	c.*1336G>A		3_prime_UTR_variant	6/6	1	NM_033201.3	ENSP00000300006.4
BMERB1	ENST00000565857.1	c.272-2865G>A		intron_variant		4		ENSP00000456084.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109754 AN: 151920 Hom.: 40451 Cov.: 32

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: 9 AN: 10 Hom.: 4 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.723 AC: 109870 AN: 152038 Hom.: 40507 Cov.: 32 AF XY: 0.724 AC XY: 53794 AN XY: 74310

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.709

Alfa AF: 0.646 Hom.: 10338

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.66

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

LitVar

Other links and lift over

dbSNP: rs1127293; hg19: chr16-15682022;