chr11-22623867-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022725.4(FANCF):​c.*819C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 188,056 control chromosomes in the GnomAD database, including 89,128 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71557 hom., cov: 30)
Exomes 𝑓: 0.99 ( 17571 hom. )

Consequence

FANCF
NM_022725.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.840
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 11-22623867-G-A is Benign according to our data. Variant chr11-22623867-G-A is described in ClinVar as [Benign]. Clinvar id is 304185.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FANCFNM_022725.4 linkuse as main transcriptc.*819C>T 3_prime_UTR_variant 1/1 ENST00000327470.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FANCFENST00000327470.6 linkuse as main transcriptc.*819C>T 3_prime_UTR_variant 1/1 NM_022725.4 P1

Frequencies

GnomAD3 genomes
AF:
0.969
AC:
147329
AN:
152078
Hom.:
71517
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.903
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.991
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
0.921
Gnomad SAS
AF:
0.972
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.994
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.977
GnomAD4 exome
AF:
0.990
AC:
35493
AN:
35860
Hom.:
17571
Cov.:
0
AF XY:
0.990
AC XY:
16523
AN XY:
16698
show subpopulations
Gnomad4 AFR exome
AF:
0.916
Gnomad4 AMR exome
AF:
0.994
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.971
Gnomad4 SAS exome
AF:
0.971
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
Gnomad4 OTH exome
AF:
0.984
GnomAD4 genome
AF:
0.969
AC:
147426
AN:
152196
Hom.:
71557
Cov.:
30
AF XY:
0.969
AC XY:
72116
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.903
Gnomad4 AMR
AF:
0.992
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
0.921
Gnomad4 SAS
AF:
0.972
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
0.976
Alfa
AF:
0.983
Hom.:
8569
Bravo
AF:
0.966
Asia WGS
AF:
0.951
AC:
3308
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Fanconi anemia complementation group F Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.0
DANN
Benign
0.92

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: rs450946; hg19: chr11-22645413; API