16-15592724-T-C

Variant names:

• chr16-15592724-T-C
• rs1107143
• ENST00000565857.1:c.*12+1609T>C

Variant summary

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

The ENST00000565857.1(BMERB1):​c.*12+1609T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,934 control chromosomes in the GnomAD database, including 40,235 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 0.72 (40235 hom., cov: 30)
• Consequence: BMERB1 ENST00000565857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMERB1	ENST00000565857.1	c.*12+1609T>C		intron_variant	Intron 4 of 4	4		ENSP00000456084.1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109359 AN: 151816 Hom.: 40180 Cov.: 30

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.721 AC: 109476 AN: 151934 Hom.: 40235 Cov.: 30 AF XY: 0.721 AC XY: 53564 AN XY: 74244

African (AFR) AF: 0.886 AC: 36724 AN: 41456

American (AMR) AF: 0.700 AC: 10682 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3260 AN: 5148

South Asian (SAS) AF: 0.759 AC: 3660 AN: 4824

European-Finnish (FIN) AF: 0.662 AC: 6983 AN: 10542

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43284 AN: 67908

Other (OTH) AF: 0.709 AC: 1499 AN: 2114

Alfa AF: 0.693 Hom.: 4616

Bravo AF: 0.727

Asia WGS AF: 0.700 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1107143; hg19: chr16-15686581;