rs9930648

Positions:

• chr16-15546958-G-C
• chr16-15546958-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033201.3(BMERB1):​c.231-21025G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,194 control chromosomes in the GnomAD database, including 11,633 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 0.35 (11633 hom., cov: 31)
• Consequence: BMERB1 NM_033201.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMERB1	NM_033201.3	c.231-21025G>C		intron_variant		ENST00000300006.9
MPV17L-BMERB1	NM_001414674.1	c.435-21025G>C		intron_variant
BMERB1	NM_001142469.2	c.180-21025G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMERB1	ENST00000300006.9	c.231-21025G>C		intron_variant		1	NM_033201.3	P1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52580 AN: 151092 Hom.: 11595 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.348 AC: 52673 AN: 151194 Hom.: 11633 Cov.: 31 AF XY: 0.353 AC XY: 26036 AN XY: 73788

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.301

Alfa AF: 0.286 Hom.: 987

Bravo AF: 0.368

Asia WGS AF: 0.446 AC: 1549 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	0.82
DANN	Benign	0.24

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: rs9930648; hg19: chr16-15640815;