21-39197853-G-A

Position:

• chr21-39197853-G-A

Variant summary

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

The NM_033656.4(BRWD1):​c.5654-438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,274 control chromosomes in the GnomAD database, including 65,763 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 0.93 (65763 hom., cov: 31)
• Consequence: BRWD1 NM_033656.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

Genes affected

BRWD1 (HGNC:12760): (bromodomain and WD repeat domain containing 1) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) residues which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein contains 2 bromodomains and multiple WD repeats. This gene is located within the Down syndrome region-2 on chromosome 21. Alternative splicing of this gene generates multiple transcript variants encoding distinct isoforms. In mouse, this gene encodes a nuclear protein that has a polyglutamine-containing region that functions as a transcriptional activation domain which may regulate chromatin remodelling and associates with a component of the SWI/SNF chromatin remodelling complex.[provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRWD1	NM_033656.4	c.5654-438C>T		intron_variant		ENST00000342449.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRWD1	ENST00000342449.8	c.5654-438C>T		intron_variant		1	NM_033656.4	A2
BRWD1	ENST00000333229.6	c.5654-438C>T		intron_variant		1		P2
BRWD1	ENST00000380800.7	c.5654-438C>T		intron_variant		1		A2
BRWD1	ENST00000446924.5	c.*1978-438C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.927 AC: 141033 AN: 152156 Hom.: 65710 Cov.: 31

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.927 AC: 141145 AN: 152274 Hom.: 65763 Cov.: 31 AF XY: 0.924 AC XY: 68777 AN XY: 74470

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.921

Alfa AF: 0.927 Hom.: 66486

Bravo AF: 0.929

Asia WGS AF: 0.739 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.19

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: rs2150410; hg19: chr21-40569779;