chr16-15508509-G-A

Position:

• chr16-15508509-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.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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMERB1	NM_033201.3	c.107-6796G>A		intron_variant		ENST00000300006.9
MPV17L-BMERB1	NM_001414674.1	c.311-6796G>A		intron_variant
LOC105371102	XR_933129.3	n.206-3750C>T		intron_variant, non_coding_transcript_variant
BMERB1	NM_001142469.2	c.55+6133G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMERB1	ENST00000300006.9	c.107-6796G>A		intron_variant		1	NM_033201.3	P1

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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.637

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.45

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: rs153783; hg19: chr16-15602366;