rs184385334
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBS1BS2_Supporting
The NM_001018113.3(FANCB):c.2165+10A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,123,235 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.000063 ( 0 hom., 2 hem., cov: 23)
Exomes 𝑓: 0.00011 ( 0 hom. 30 hem. )
Consequence
FANCB
NM_001018113.3 intron
NM_001018113.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.523
Genes affected
FANCB (HGNC:3583): (FA complementation group B) This gene encodes a member of the Fanconi anemia complementation group B. This protein is assembled into a nucleoprotein complex that is involved in the repair of DNA lesions. Mutations in this gene can cause chromosome instability and VACTERL syndrome with hydrocephalus. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant X-14844493-T-A is Benign according to our data. Variant chrX-14844493-T-A is described in ClinVar as [Benign]. Clinvar id is 456182.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000626 (7/111819) while in subpopulation EAS AF= 0.00197 (7/3556). AF 95% confidence interval is 0.000924. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd4 at 2 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.2165+10A>T | intron_variant | ENST00000650831.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCB | ENST00000650831.1 | c.2165+10A>T | intron_variant | NM_001018113.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000626 AC: 7AN: 111766Hom.: 0 Cov.: 23 AF XY: 0.0000590 AC XY: 2AN XY: 33918
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GnomAD3 exomes AF: 0.000341 AC: 62AN: 181976Hom.: 0 AF XY: 0.000238 AC XY: 16AN XY: 67102
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GnomAD4 exome AF: 0.000111 AC: 112AN: 1011416Hom.: 0 Cov.: 21 AF XY: 0.0000995 AC XY: 30AN XY: 301616
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GnomAD4 genome ? AF: 0.0000626 AC: 7AN: 111819Hom.: 0 Cov.: 23 AF XY: 0.0000589 AC XY: 2AN XY: 33981
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Fanconi anemia complementation group B Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Fanconi anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at