rs1125972

Variant names:

• chr16-15513130-A-G
• rs1125972
• NM_033201.3:c.107-2175A>G

Variant summary

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

The NM_033201.3(BMERB1):​c.107-2175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,134 control chromosomes in the GnomAD database, including 540 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 0.069 (540 hom., cov: 32)
• Consequence: BMERB1 NM_033201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMERB1	NM_033201.3	c.107-2175A>G		intron_variant	Intron 1 of 5	ENST00000300006.9	NP_149978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMERB1	ENST00000300006.9	c.107-2175A>G		intron_variant	Intron 1 of 5	1	NM_033201.3	ENSP00000300006.4
ENSG00000261130	ENST00000568766.1	c.311-2175A>G		intron_variant	Intron 1 of 1	2		ENSP00000454340.1

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10565 AN: 152016 Hom.: 541 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0695 AC: 10568 AN: 152134 Hom.: 540 Cov.: 32 AF XY: 0.0735 AC XY: 5464 AN XY: 74364

African (AFR) AF: 0.0166 AC: 690 AN: 41538

American (AMR) AF: 0.149 AC: 2277 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3468

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5166

South Asian (SAS) AF: 0.103 AC: 499 AN: 4822

European-Finnish (FIN) AF: 0.0990 AC: 1048 AN: 10584

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5612 AN: 67990

Other (OTH) AF: 0.0662 AC: 140 AN: 2116

Alfa AF: 0.0797 Hom.: 1479

Bravo AF: 0.0708

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.58
PhyloP100		-1.3
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: rs1125972; hg19: chr16-15606987;