rs1065838

Variant names:

• chr16-15534181-G-A
• rs1065838
• NM_033201.3:c.230+18753G>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.230+18753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 150,760 control chromosomes in the GnomAD database, including 46,915 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 0.79 (46915 hom., cov: 25)
• Consequence: BMERB1 NM_033201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 1 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]

MPV17L-BMERB1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMERB1	NM_033201.3	c.230+18753G>A		intron_variant	Intron 2 of 5	ENST00000300006.9	NP_149978.1
MPV17L-BMERB1	NM_001414674.1	c.434+18753G>A		intron_variant	Intron 2 of 5		NP_001401603.1
BMERB1	NM_001142469.2	c.179+18753G>A		intron_variant	Intron 2 of 5		NP_001135941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMERB1	ENST00000300006.9	c.230+18753G>A		intron_variant	Intron 2 of 5	1	NM_033201.3	ENSP00000300006.4

Frequencies

GnomAD3 genomes AF: 0.785 AC: 118293 AN: 150646 Hom.: 46854 Cov.: 25

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.785 AC: 118415 AN: 150760 Hom.: 46915 Cov.: 25 AF XY: 0.789 AC XY: 57999 AN XY: 73506

African (AFR) AF: 0.910 AC: 37449 AN: 41156

American (AMR) AF: 0.825 AC: 12438 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2437 AN: 3462

East Asian (EAS) AF: 0.617 AC: 3110 AN: 5038

South Asian (SAS) AF: 0.765 AC: 3623 AN: 4734

European-Finnish (FIN) AF: 0.784 AC: 8075 AN: 10306

Middle Eastern (MID) AF: 0.755 AC: 219 AN: 290

European-Non Finnish (NFE) AF: 0.720 AC: 48737 AN: 67710

Other (OTH) AF: 0.763 AC: 1586 AN: 2078

Alfa AF: 0.740 Hom.: 77583

Bravo AF: 0.792

Asia WGS AF: 0.689 AC: 2398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.27
PhyloP100		-2.1
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: rs1065838; hg19: chr16-15628038;