Variant rs16942918 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000310775.12(FANCI):c.288+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,606,636 control chromosomes in the GnomAD database, including 133,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17674 hom., cov: 31)

Exomes 𝑓: 0.39 ( 115633 hom. )

Consequence

FANCI
ENST00000310775.12 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.236

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=-0.91).

BP6

Variant 15-89260880-G-A is Benign according to our data. Variant chr15-89260880-G-A is described in ClinVar as [Benign]. Clinvar id is 257486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FANCI	NM_001113378.2 linkuse as main transcript	c.288+37G>A		intron_variant		ENST00000310775.12	NP_001106849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FANCI	ENST00000310775.12 linkuse as main transcript	c.288+37G>A		intron_variant		1	NM_001113378.2	ENSP00000310842	P1	Q9NVI1-3

Frequencies

GnomAD3 genomes

AF:

0.468

AC:

70962

AN:

151776

Hom.:

17647

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.377

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.435

GnomAD3 exomes

AF:

0.411

AC:

103140

AN:

250888

Hom.:

22015

AF XY:

0.408

AC XY:

55356

AN XY:

135674

show subpopulations

Gnomad AFR exome

AF:

0.650

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.390

Gnomad EAS exome

AF:

0.339

Gnomad SAS exome

AF:

0.389

Gnomad FIN exome

AF:

0.484

Gnomad NFE exome

AF:

0.386

Gnomad OTH exome

AF:

0.398

GnomAD4 exome

AF:

0.394

AC:

573701

AN:

1454742

Hom.:

115633

Cov.:

AF XY:

0.394

AC XY:

285051

AN XY:

723768

show subpopulations

Gnomad4 AFR exome

AF:

0.657

Gnomad4 AMR exome

AF:

0.398

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.324

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.477

Gnomad4 NFE exome

AF:

0.384

Gnomad4 OTH exome

AF:

0.409

GnomAD4 genome

AF:

0.468

AC:

71030

AN:

151894

Hom.:

17674

Cov.:

AF XY:

0.470

AC XY:

34899

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.651

Gnomad4 AMR

AF:

0.389

Gnomad4 ASJ

AF:

0.377

Gnomad4 EAS

AF:

0.338

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.393

Gnomad4 OTH

AF:

0.431

Alfa

AF:

0.398

Hom.:

20155

Bravo

AF:

0.472

Asia WGS

AF:

0.370

AC:

1287

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Fanconi anemia complementation group I

Benign:2

Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.21

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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