rs754552650
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001018113.3(FANCB):c.869T>C(p.Met290Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000197 in 1,208,243 control chromosomes in the GnomAD database, including 1 homozygotes. There are 89 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., 10 hem., cov: 23)
Exomes 𝑓: 0.00020 ( 1 hom. 79 hem. )
Consequence
FANCB
NM_001018113.3 missense
NM_001018113.3 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 4.53
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.007908583).
BP6
?
Variant X-14864642-A-G is Benign according to our data. Variant chrX-14864642-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 368030.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 = 0.000178 (20/112499) while in subpopulation EAS AF= 0.00363 (13/3579). AF 95% confidence interval is 0.00215. There are 0 homozygotes in gnomad4. There are 10 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd at 10 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCB | NM_001018113.3 | c.869T>C | p.Met290Thr | missense_variant | 3/10 | ENST00000650831.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCB | ENST00000650831.1 | c.869T>C | p.Met290Thr | missense_variant | 3/10 | NM_001018113.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 20AN: 112448Hom.: 0 Cov.: 23 AF XY: 0.000289 AC XY: 10AN XY: 34590
GnomAD3 genomes
?
AF:
AC:
20
AN:
112448
Hom.:
Cov.:
23
AF XY:
AC XY:
10
AN XY:
34590
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000453 AC: 83AN: 183393Hom.: 1 AF XY: 0.000486 AC XY: 33AN XY: 67859
GnomAD3 exomes
AF:
AC:
83
AN:
183393
Hom.:
AF XY:
AC XY:
33
AN XY:
67859
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000199 AC: 218AN: 1095744Hom.: 1 Cov.: 30 AF XY: 0.000219 AC XY: 79AN XY: 361164
GnomAD4 exome
AF:
AC:
218
AN:
1095744
Hom.:
Cov.:
30
AF XY:
AC XY:
79
AN XY:
361164
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000178 AC: 20AN: 112499Hom.: 0 Cov.: 23 AF XY: 0.000289 AC XY: 10AN XY: 34651
GnomAD4 genome
?
AF:
AC:
20
AN:
112499
Hom.:
Cov.:
23
AF XY:
AC XY:
10
AN XY:
34651
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
1
ALSPAC
AF:
AC:
0
ExAC
?
AF:
AC:
52
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Fanconi anemia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Mar 10, 2022 | - - |
VACTERL with hydrocephalus Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
FANCB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 02, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Fanconi Anemia, X-Linked Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;P;.
Vest4
MutPred
Loss of stability (P = 0.0295);Loss of stability (P = 0.0295);Loss of stability (P = 0.0295);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at