Variant X-14782377-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000696352.1(FANCB):c.*107+13783A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 15858 hom., 19826 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

FANCB
ENST00000696352.1 intron, NMD_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.474

Variant links:

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]

FANCB links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
FANCB	XR_001755672.2 linkuse as main transcript	n.3172+13783A>G	intron_variant, non_coding_transcript_variant
FANCB	XR_001755673.2 linkuse as main transcript	n.7114+13783A>G	intron_variant, non_coding_transcript_variant
FANCB	XR_001755674.2 linkuse as main transcript	n.3051+13783A>G	intron_variant, non_coding_transcript_variant
FANCB	XR_007068184.1 linkuse as main transcript	n.3151+13783A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FANCB	ENST00000696351.1 linkuse as main transcript	c.*514+13783A>G		intron_variant, NMD_transcript_variant
FANCB	ENST00000696352.1 linkuse as main transcript	c.*107+13783A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.623

AC:

68700

AN:

110230

Hom.:

15864

Cov.:

AF XY:

0.609

AC XY:

19781

AN XY:

32470

show subpopulations

Gnomad AFR

AF:

0.753

Gnomad AMI

AF:

0.870

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.608

Gnomad MID

AF:

0.603

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.580

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.623

AC:

68730

AN:

110280

Hom.:

15858

Cov.:

AF XY:

0.609

AC XY:

19826

AN XY:

32530

show subpopulations

Gnomad4 AFR

AF:

0.754

Gnomad4 AMR

AF:

0.520

Gnomad4 ASJ

AF:

0.552

Gnomad4 EAS

AF:

0.184

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.608

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.576

Alfa

AF:

0.637

Hom.:

7901

Bravo

AF:

0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

DANN

Benign

0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over