chrX-80670583-T-TA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_153252.5(BRWD3):c.*6025_*6026insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 107,242 control chromosomes in the GnomAD database, including 21 homozygotes. There are 445 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.017 ( 21 hom., 445 hem., cov: 21)
Consequence
BRWD3
NM_153252.5 3_prime_UTR
NM_153252.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.846
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 -10 ACMG points.
BP6
?
Variant X-80670583-T-TA is Benign according to our data. Variant chrX-80670583-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 368686.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0173 (1851/107242) while in subpopulation NFE AF= 0.0276 (1426/51688). AF 95% confidence interval is 0.0264. There are 21 homozygotes in gnomad4. There are 445 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 21 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRWD3 | NM_153252.5 | c.*6025_*6026insT | 3_prime_UTR_variant | 41/41 | ENST00000373275.5 | ||
BRWD3 | XM_005262113.4 | c.*6025_*6026insT | 3_prime_UTR_variant | 40/40 | |||
BRWD3 | XM_017029384.2 | c.*6025_*6026insT | 3_prime_UTR_variant | 30/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRWD3 | ENST00000373275.5 | c.*6025_*6026insT | 3_prime_UTR_variant | 41/41 | 1 | NM_153252.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0173 AC: 1851AN: 107214Hom.: 21 Cov.: 21 AF XY: 0.0146 AC XY: 445AN XY: 30376
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GnomAD4 genome ? AF: 0.0173 AC: 1851AN: 107242Hom.: 21 Cov.: 21 AF XY: 0.0146 AC XY: 445AN XY: 30418
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Non-syndromic X-linked intellectual disability Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at