rs150393409

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_014967.5(FAN1):​c.1520G>A​(p.Arg507His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0089 in 1,614,058 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0060 ( 4 hom., cov: 33)
Exomes 𝑓: 0.0092 ( 82 hom. )

Consequence

FAN1
NM_014967.5 missense

Scores

6
13

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: 3.43
Variant links:
Genes affected
FAN1 (HGNC:29170): (FANCD2 and FANCI associated nuclease 1) This gene plays a role in DNA interstrand cross-link repair and encodes a protein with 5' flap endonuclease and 5'-3' exonuclease activity. Mutations in this gene cause karyomegalic interstitial nephritis. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Feb 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.008552343).
BP6
Variant 15-30910758-G-A is Benign according to our data. Variant chr15-30910758-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 619975.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Benign=1, Uncertain_significance=1}. Variant chr15-30910758-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00604 (920/152208) while in subpopulation NFE AF= 0.0099 (673/68004). AF 95% confidence interval is 0.00928. There are 4 homozygotes in gnomad4. There are 404 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAN1NM_014967.5 linkc.1520G>A p.Arg507His missense_variant Exon 4 of 15 ENST00000362065.9 NP_055782.3 Q9Y2M0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAN1ENST00000362065.9 linkc.1520G>A p.Arg507His missense_variant Exon 4 of 15 1 NM_014967.5 ENSP00000354497.4 Q9Y2M0-1

Frequencies

GnomAD3 genomes
AF:
0.00605
AC:
920
AN:
152090
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00155
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00458
Gnomad ASJ
AF:
0.00605
Gnomad EAS
AF:
0.000578
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.00538
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00990
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00656
AC:
1649
AN:
251456
Hom.:
11
AF XY:
0.00684
AC XY:
930
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.00135
Gnomad AMR exome
AF:
0.00474
Gnomad ASJ exome
AF:
0.0106
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00408
Gnomad FIN exome
AF:
0.00430
Gnomad NFE exome
AF:
0.00964
Gnomad OTH exome
AF:
0.00636
GnomAD4 exome
AF:
0.00920
AC:
13449
AN:
1461850
Hom.:
82
Cov.:
32
AF XY:
0.00906
AC XY:
6589
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.00164
Gnomad4 AMR exome
AF:
0.00476
Gnomad4 ASJ exome
AF:
0.0105
Gnomad4 EAS exome
AF:
0.00146
Gnomad4 SAS exome
AF:
0.00348
Gnomad4 FIN exome
AF:
0.00444
Gnomad4 NFE exome
AF:
0.0106
Gnomad4 OTH exome
AF:
0.00772
GnomAD4 genome
AF:
0.00604
AC:
920
AN:
152208
Hom.:
4
Cov.:
33
AF XY:
0.00543
AC XY:
404
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.00154
Gnomad4 AMR
AF:
0.00458
Gnomad4 ASJ
AF:
0.00605
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.00270
Gnomad4 FIN
AF:
0.00538
Gnomad4 NFE
AF:
0.00990
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00775
Hom.:
6
Bravo
AF:
0.00624
TwinsUK
AF:
0.0121
AC:
45
ALSPAC
AF:
0.0104
AC:
40
ESP6500AA
AF:
0.00136
AC:
6
ESP6500EA
AF:
0.00791
AC:
68
ExAC
AF:
0.00619
AC:
751
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.00965
EpiControl
AF:
0.0119

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Benign:2
Jan 22, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

FAN1: BP4, BS2 -

Karyomegalic interstitial nephritis Uncertain:1
Mar 16, 2018
Center for Precision Medicine, Vanderbilt University Medical Center
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
.;T;.;.
Eigen
Benign
-0.050
Eigen_PC
Benign
-0.049
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.89
.;D;.;D
M_CAP
Benign
0.019
T
MetaRNN
Benign
0.0086
T;T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.3
M;M;M;M
PrimateAI
Benign
0.27
T
PROVEAN
Uncertain
-2.8
D;N;D;D
REVEL
Benign
0.11
Sift
Benign
0.030
D;D;D;D
Sift4G
Uncertain
0.048
D;T;D;D
Polyphen
0.91
P;P;P;P
Vest4
0.15
MVP
0.43
MPC
0.47
ClinPred
0.019
T
GERP RS
2.6
Varity_R
0.21
gMVP
0.25

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: rs150393409; hg19: chr15-31202961; COSMIC: COSV100755790; COSMIC: COSV100755790; API