chrX-80670278-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000373275.5(BRWD3):c.*6331C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 110,691 control chromosomes in the GnomAD database, including 1,149 homozygotes. There are 5,511 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 1149 hom., 5511 hem., cov: 21)
Consequence
BRWD3
ENST00000373275.5 3_prime_UTR
ENST00000373275.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.665
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant X-80670278-G-C is Benign according to our data. Variant chrX-80670278-G-C is described in ClinVar as [Benign]. Clinvar id is 914166.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BRWD3 | NM_153252.5 | c.*6331C>G | 3_prime_UTR_variant | 41/41 | ENST00000373275.5 | NP_694984.5 | ||
BRWD3 | XM_005262113.4 | c.*6331C>G | 3_prime_UTR_variant | 40/40 | XP_005262170.1 | |||
BRWD3 | XM_017029384.2 | c.*6331C>G | 3_prime_UTR_variant | 30/30 | XP_016884873.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRWD3 | ENST00000373275.5 | c.*6331C>G | 3_prime_UTR_variant | 41/41 | 1 | NM_153252.5 | ENSP00000362372 | P1 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 18206AN: 110638Hom.: 1151 Cov.: 21 AF XY: 0.167 AC XY: 5501AN XY: 32910
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.165 AC: 18217AN: 110691Hom.: 1149 Cov.: 21 AF XY: 0.167 AC XY: 5511AN XY: 32973
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked 93 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at