3-46979842-G-GGCCGGA
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS1_Supporting
The NM_015175.3(NBEAL2):c.-14_-9dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 441,060 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0011 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 1 hom. )
Consequence
NBEAL2
NM_015175.3 5_prime_UTR
NM_015175.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.25
Genes affected
NBEAL2 (HGNC:31928): (neurobeachin like 2) The protein encoded by this gene contains a beige and Chediak-Higashi (BEACH) domain and multiple WD40 domains, and may play a role in megakaryocyte alpha-granule biogenesis. Mutations in this gene are a cause of gray platelet syndrome. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00109 (165/151852) while in subpopulation AMR AF= 0.0036 (55/15262). AF 95% confidence interval is 0.00284. There are 1 homozygotes in gnomad4. There are 77 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBEAL2 | NM_015175.3 | c.-14_-9dup | 5_prime_UTR_variant | 1/54 | ENST00000450053.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBEAL2 | ENST00000450053.8 | c.-14_-9dup | 5_prime_UTR_variant | 1/54 | 2 | NM_015175.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00109 AC: 165AN: 151744Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000565 AC: 12AN: 21252Hom.: 0 AF XY: 0.000831 AC XY: 11AN XY: 13244
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GnomAD4 exome AF: 0.00120 AC: 347AN: 289208Hom.: 1 Cov.: 0 AF XY: 0.00125 AC XY: 197AN XY: 158018
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GnomAD4 genome AF: 0.00109 AC: 165AN: 151852Hom.: 1 Cov.: 33 AF XY: 0.00104 AC XY: 77AN XY: 74258
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Gray platelet syndrome Uncertain:1
Uncertain significance, 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