16-15508509-G-A

Variant names:

• chr16-15508509-G-A
• rs153783
• NM_033201.3:c.107-6796G>A

Variant summary

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

The NM_033201.3(BMERB1):​c.107-6796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,836 control chromosomes in the GnomAD database, including 26,851 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 0.57 (26851 hom., cov: 30)
• Consequence: BMERB1 NM_033201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 2 publications found

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]

ENSG00000261130 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.708 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMERB1	NM_033201.3	MANE Select	c.107-6796G>A		intron	N/A	NP_149978.1
	MPV17L-BMERB1	NM_001414674.1		c.311-6796G>A		intron	N/A	NP_001401603.1
	BMERB1	NM_001142469.2		c.55+6133G>A		intron	N/A	NP_001135941.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMERB1	ENST00000300006.9	TSL:1 MANE Select	c.107-6796G>A		intron	N/A	ENSP00000300006.4
	BMERB1	ENST00000452191.6	TSL:1	c.55+6133G>A		intron	N/A	ENSP00000408976.2
	ENSG00000261130	ENST00000568766.1	TSL:2	c.311-6796G>A		intron	N/A	ENSP00000454340.1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86397 AN: 151722 Hom.: 26845 Cov.: 30

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.631

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.569 AC: 86419 AN: 151836 Hom.: 26851 Cov.: 30 AF XY: 0.563 AC XY: 41782 AN XY: 74200

African (AFR) AF: 0.332 AC: 13758 AN: 41380

American (AMR) AF: 0.496 AC: 7563 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2755 AN: 3462

East Asian (EAS) AF: 0.454 AC: 2343 AN: 5156

South Asian (SAS) AF: 0.543 AC: 2615 AN: 4812

European-Finnish (FIN) AF: 0.642 AC: 6762 AN: 10536

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48455 AN: 67932

Other (OTH) AF: 0.637 AC: 1339 AN: 2102

Alfa AF: 0.594 Hom.: 3782

Bravo AF: 0.546

Asia WGS AF: 0.505 AC: 1755 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	0.39
DANN	Benign	0.45
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs153783; hg19: chr16-15602366;