rs1125972

Positions:

• chr16-15513130-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
BMERB1	NM_033201.3	c.107-2175A>G		intron_variant		ENST00000300006.9
MPV17L-BMERB1	NM_001414674.1	c.311-2175A>G		intron_variant
LOC105371102	XR_933129.3	n.205+180T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMERB1	ENST00000300006.9	c.107-2175A>G		intron_variant		1	NM_033201.3	P1

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

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0843 Hom.: 917

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

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: rs1125972; hg19: chr16-15606987;