rs9924674

Variant names:

• chr16-15572423-T-C
• rs9924674
• NM_033201.3:c.304+4367T>C

Variant summary

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

The NM_033201.3(BMERB1):​c.304+4367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,220 control chromosomes in the GnomAD database, including 1,582 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 0.083 (1582 hom., cov: 32)
• Consequence: BMERB1 NM_033201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMERB1	NM_033201.3	c.304+4367T>C		intron_variant	Intron 3 of 5	ENST00000300006.9	NP_149978.1
MPV17L-BMERB1	NM_001414674.1	c.508+4367T>C		intron_variant	Intron 3 of 5		NP_001401603.1
BMERB1	NM_001142469.2	c.253+4367T>C		intron_variant	Intron 3 of 5		NP_001135941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMERB1	ENST00000300006.9	c.304+4367T>C		intron_variant	Intron 3 of 5	1	NM_033201.3	ENSP00000300006.4

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12626 AN: 152102 Hom.: 1573 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00451

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0832 AC: 12668 AN: 152220 Hom.: 1582 Cov.: 32 AF XY: 0.0818 AC XY: 6087 AN XY: 74438

African (AFR) AF: 0.272 AC: 11276 AN: 41498

American (AMR) AF: 0.0407 AC: 623 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3470

East Asian (EAS) AF: 0.00502 AC: 26 AN: 5182

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4828

European-Finnish (FIN) AF: 0.0108 AC: 115 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00451 AC: 307 AN: 68024

Other (OTH) AF: 0.0739 AC: 156 AN: 2112

Alfa AF: 0.0316 Hom.: 170

Bravo AF: 0.0928

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.54
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: rs9924674; hg19: chr16-15666280;