rs11266586

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_153252.5(BRWD3):​c.*6331C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 110,734 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. 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 0.00024 ( 0 hom., 10 hem., cov: 21)

Consequence

BRWD3
NM_153252.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.665
Variant links:
Genes affected
BRWD3 (HGNC:17342): (bromodomain and WD repeat domain containing 3) The protein encoded by this gene contains a bromodomain and several WD repeats. It is thought to have a chromatin-modifying function, and may thus play a role in transcription. Mutations in this gene are associated with a spectrum of cognitive disabilities and X-linked macrocephaly. This gene is also associated with translocations in patients with B-cell chronic lymphocytic leukemia. [provided by RefSeq, Jul 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BS2
High Hemizygotes in GnomAd4 at 10 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BRWD3NM_153252.5 linkc.*6331C>T 3_prime_UTR_variant Exon 41 of 41 ENST00000373275.5 NP_694984.5 Q6RI45-1
BRWD3XM_005262113.4 linkc.*6331C>T 3_prime_UTR_variant Exon 40 of 40 XP_005262170.1
BRWD3XM_017029384.2 linkc.*6331C>T 3_prime_UTR_variant Exon 30 of 30 XP_016884873.1 Q6RI45-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BRWD3ENST00000373275 linkc.*6331C>T 3_prime_UTR_variant Exon 41 of 41 1 NM_153252.5 ENSP00000362372.4 Q6RI45-1

Frequencies

GnomAD3 genomes
AF:
0.000244
AC:
27
AN:
110681
Hom.:
0
Cov.:
21
AF XY:
0.000273
AC XY:
9
AN XY:
32929
show subpopulations
Gnomad AFR
AF:
0.000658
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000244
AC:
27
AN:
110734
Hom.:
0
Cov.:
21
AF XY:
0.000303
AC XY:
10
AN XY:
32992
show subpopulations
Gnomad4 AFR
AF:
0.000657
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.023
DANN
Benign
0.44

Splicing

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: rs11266586; hg19: chrX-79925777; API