X-14782377-T-C

Variant names:

• chrX-14782377-T-C
• rs3020867
• ENST00000696351.1:n.*514+13783A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000696351.1(FANCB):​n.*514+13783A>G variant causes a intron 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 ENST00000696351.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• Fanconi anemia complementation group B

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
• VACTERL association, X-linked, with or without hydrocephalus

  Inheritance: XL Classification: STRONG Submitted by: Genomics England PanelApp
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• VACTERL with hydrocephalus

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000696351.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FANCB	ENST00000696351.1		n.*514+13783A>G		intron	N/A	ENSP00000512572.1
	FANCB	ENST00000696352.1		n.*107+13783A>G		intron	N/A	ENSP00000512573.1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 68700 AN: 110230 Hom.: 15864 Cov.: 22

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.: 22 AF XY: 0.609 AC XY: 19826 AN XY: 32530

African (AFR) AF: 0.754 AC: 22838 AN: 30308

American (AMR) AF: 0.520 AC: 5422 AN: 10428

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1455 AN: 2637

East Asian (EAS) AF: 0.184 AC: 640 AN: 3481

South Asian (SAS) AF: 0.415 AC: 1080 AN: 2603

European-Finnish (FIN) AF: 0.608 AC: 3494 AN: 5750

Middle Eastern (MID) AF: 0.610 AC: 130 AN: 213

European-Non Finnish (NFE) AF: 0.612 AC: 32216 AN: 52678

Other (OTH) AF: 0.576 AC: 868 AN: 1507

Alfa AF: 0.637 Hom.: 7901

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3020867; hg19: chrX-14800499;