rs9930648

Variant names:

• chr16-15546958-G-C
• rs9930648
• NM_033201.3:c.231-21025G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033201.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMERB1	NM_033201.3	MANE Select	c.231-21025G>C		intron	N/A	NP_149978.1	Q96MC5-1
	MPV17L-BMERB1	NM_001414674.1		c.435-21025G>C		intron	N/A	NP_001401603.1
	BMERB1	NM_001142469.2		c.180-21025G>C		intron	N/A	NP_001135941.1	Q96MC5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMERB1	ENST00000300006.9	TSL:1 MANE Select	c.231-21025G>C		intron	N/A	ENSP00000300006.4	Q96MC5-1
	BMERB1	ENST00000452191.6	TSL:1	c.180-21025G>C		intron	N/A	ENSP00000408976.2	Q96MC5-2
	BMERB1	ENST00000869050.1		c.225-21025G>C		intron	N/A	ENSP00000539109.1

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

African (AFR) AF: 0.613 AC: 25150 AN: 41056

American (AMR) AF: 0.349 AC: 5303 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2592 AN: 5136

South Asian (SAS) AF: 0.374 AC: 1795 AN: 4800

European-Finnish (FIN) AF: 0.271 AC: 2810 AN: 10356

Middle Eastern (MID) AF: 0.245 AC: 71 AN: 290

European-Non Finnish (NFE) AF: 0.199 AC: 13495 AN: 67902

Other (OTH) AF: 0.301 AC: 629 AN: 2088

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.24
PhyloP100		-0.76
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: rs9930648; hg19: chr16-15640815;