rs1065838

chr16-15534181-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
BMERB1	NM_033201.3	c.230+18753G>A		intron_variant		ENST00000300006.9
MPV17L-BMERB1	NM_001414674.1	c.434+18753G>A		intron_variant
BMERB1	NM_001142469.2	c.179+18753G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMERB1	ENST00000300006.9	c.230+18753G>A		intron_variant		1	NM_033201.3	P1

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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.763

Alfa AF: 0.733 Hom.: 54623

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

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: rs1065838; hg19: chr16-15628038;