rs1981624

Variant names:

Variant summary

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

The NM_001113378.2(FANCI):c.545+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,561,272 control chromosomes in the GnomAD database, including 110,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10604 hom., cov: 32)

Exomes 𝑓: 0.37 ( 99805 hom. )

Consequence

FANCI
NM_001113378.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.38

Variant links:

Genes affected

FANCI (HGNC:25568): (FA complementation group I) 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 I. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

FANCI links:

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=-0.89).

BP6

Variant 15-89263490-G-A is Benign according to our data. Variant chr15-89263490-G-A is described in ClinVar as [Benign]. Clinvar id is 257491.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FANCI	NM_001113378.2 link	c.545+30G>A		intron_variant	Intron 7 of 37	ENST00000310775.12	NP_001106849.1	Q9NVI1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FANCI	ENST00000310775.12 link	c.545+30G>A		intron_variant	Intron 7 of 37	1	NM_001113378.2	ENSP00000310842.8		Q9NVI1-3

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56363

AN:

151792

Hom.:

10599

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.368

GnomAD3 exomes

AF:

0.381

AC:

95314

AN:

250266

Hom.:

18502

AF XY:

0.384

AC XY:

51946

AN XY:

135306

show subpopulations

Gnomad AFR exome

AF:

0.326

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.381

Gnomad EAS exome

AF:

0.323

Gnomad SAS exome

AF:

0.384

Gnomad FIN exome

AF:

0.459

Gnomad NFE exome

AF:

0.382

Gnomad OTH exome

AF:

0.380

GnomAD4 exome

AF:

0.373

AC:

525288

AN:

1409362

Hom.:

99805

Cov.:

AF XY:

0.375

AC XY:

263690

AN XY:

704002

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.377

Gnomad4 ASJ exome

AF:

0.381

Gnomad4 EAS exome

AF:

0.308

Gnomad4 SAS exome

AF:

0.382

Gnomad4 FIN exome

AF:

0.453

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.377

GnomAD4 genome

AF:

0.371

AC:

56394

AN:

151910

Hom.:

10604

Cov.:

AF XY:

0.376

AC XY:

27887

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.323

Gnomad4 SAS

AF:

0.377

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.389

Gnomad4 OTH

AF:

0.366

Alfa

AF:

0.387

Hom.:

3002

Bravo

AF:

0.365

Asia WGS

AF:

0.351

AC:

1217

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fanconi anemia complementation group I

Benign:2

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.012

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over