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GeneBe

rs9981595

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033656.4(BRWD1):c.*7507A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 985,278 control chromosomes in the GnomAD database, including 8,098 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 0.10 ( 918 hom., cov: 32)
Exomes 𝑓: 0.13 ( 7180 hom. )

Consequence

BRWD1
NM_033656.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRWD1NM_033656.4 linkuse as main transcriptc.*7507A>C 3_prime_UTR_variant 41/41 ENST00000342449.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRWD1ENST00000342449.8 linkuse as main transcriptc.*7507A>C 3_prime_UTR_variant 41/411 NM_033656.4 A2Q9NSI6-2
BRWD1ENST00000333229.6 linkuse as main transcriptc.6572-1335A>C intron_variant 1 P2Q9NSI6-1
BRWD1ENST00000446924.5 linkuse as main transcriptc.*2896-1335A>C intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15451
AN:
152098
Hom.:
916
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0321
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.115
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.119
Gnomad FIN
AF:
0.132
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.131
Gnomad OTH
AF:
0.0982
GnomAD4 exome
AF:
0.130
AC:
108051
AN:
833062
Hom.:
7180
Cov.:
33
AF XY:
0.130
AC XY:
49920
AN XY:
384698
show subpopulations
Gnomad4 AFR exome
AF:
0.0201
Gnomad4 AMR exome
AF:
0.157
Gnomad4 ASJ exome
AF:
0.138
Gnomad4 EAS exome
AF:
0.147
Gnomad4 SAS exome
AF:
0.107
Gnomad4 FIN exome
AF:
0.156
Gnomad4 NFE exome
AF:
0.132
Gnomad4 OTH exome
AF:
0.130
GnomAD4 genome
AF:
0.102
AC:
15463
AN:
152216
Hom.:
918
Cov.:
32
AF XY:
0.101
AC XY:
7535
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.0322
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.120
Gnomad4 FIN
AF:
0.132
Gnomad4 NFE
AF:
0.131
Gnomad4 OTH
AF:
0.0972
Alfa
AF:
0.125
Hom.:
1089
Bravo
AF:
0.0998
Asia WGS
AF:
0.115
AC:
400
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
0.33
Dann
Benign
0.66

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9981595; hg19: chr21-40560678; API