11-22623347-A-AT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_022725.4(FANCF):​c.*1338_*1339insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.96 ( 70353 hom., cov: 0)
Exomes 𝑓: 0.98 ( 22106 hom. )

Consequence

FANCF
NM_022725.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -0.574
Variant links:
Genes affected
FANCF (HGNC:3587): (FA complementation group F) The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group F. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FANCFNM_022725.4 linkuse as main transcriptc.*1338_*1339insA 3_prime_UTR_variant 1/1 ENST00000327470.6 NP_073562.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FANCFENST00000327470.6 linkuse as main transcriptc.*1338_*1339insA 3_prime_UTR_variant 1/1 NM_022725.4 ENSP00000330875 P1

Frequencies

GnomAD3 genomes
AF:
0.961
AC:
146006
AN:
151896
Hom.:
70322
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.889
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.965
Gnomad ASJ
AF:
0.997
Gnomad EAS
AF:
0.925
Gnomad SAS
AF:
0.996
Gnomad FIN
AF:
0.980
Gnomad MID
AF:
0.991
Gnomad NFE
AF:
0.999
Gnomad OTH
AF:
0.971
GnomAD4 exome
AF:
0.975
AC:
45264
AN:
46424
Hom.:
22106
Cov.:
0
AF XY:
0.977
AC XY:
20850
AN XY:
21348
show subpopulations
Gnomad4 AFR exome
AF:
0.891
Gnomad4 AMR exome
AF:
0.945
Gnomad4 ASJ exome
AF:
0.999
Gnomad4 EAS exome
AF:
0.902
Gnomad4 SAS exome
AF:
0.991
Gnomad4 FIN exome
AF:
0.967
Gnomad4 NFE exome
AF:
0.998
Gnomad4 OTH exome
AF:
0.979
GnomAD4 genome
AF:
0.961
AC:
146093
AN:
152010
Hom.:
70353
Cov.:
0
AF XY:
0.961
AC XY:
71409
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.889
Gnomad4 AMR
AF:
0.965
Gnomad4 ASJ
AF:
0.997
Gnomad4 EAS
AF:
0.925
Gnomad4 SAS
AF:
0.996
Gnomad4 FIN
AF:
0.980
Gnomad4 NFE
AF:
0.999
Gnomad4 OTH
AF:
0.971
Alfa
AF:
0.991
Hom.:
2232

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Fanconi anemia Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs45554234; hg19: chr11-22644893; API