Variant chr15-89247480-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001113378.2(FANCI):c.-19-149A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 646,390 control chromosomes in the GnomAD database, including 2,123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.094 ( 871 hom., cov: 31)

Exomes 𝑓: 0.067 ( 1252 hom. )

Consequence

FANCI
NM_001113378.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.00

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 15-89247480-A-G is Benign according to our data. Variant chr15-89247480-A-G is described in ClinVar as [Benign]. Clinvar id is 1243727.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FANCI	NM_001113378.2 linkuse as main transcript	c.-19-149A>G		intron_variant		ENST00000310775.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FANCI	ENST00000310775.12 linkuse as main transcript	c.-19-149A>G		intron_variant		1	NM_001113378.2	P1	Q9NVI1-3

Frequencies

GnomAD3 genomes

AF:

0.0937

AC:

14249

AN:

152134

Hom.:

866

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.0633

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0826

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0713

Gnomad OTH

AF:

0.0881

GnomAD4 exome

AF:

0.0673

AC:

33257

AN:

494138

Hom.:

1252

AF XY:

0.0674

AC XY:

17798

AN XY:

263988

show subpopulations

Gnomad4 AFR exome

AF:

0.170

Gnomad4 AMR exome

AF:

0.0491

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.000154

Gnomad4 SAS exome

AF:

0.0772

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.0709

Gnomad4 OTH exome

AF:

0.0740

GnomAD4 genome

AF:

0.0937

AC:

14263

AN:

152252

Hom.:

871

Cov.:

AF XY:

0.0914

AC XY:

6802

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.170

Gnomad4 AMR

AF:

0.0632

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.0813

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0713

Gnomad4 OTH

AF:

0.0872

Alfa

AF:

0.0823

Hom.:

128

Bravo

AF:

0.0986

Asia WGS

AF:

0.0560

AC:

195

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.8

DANN

Benign

0.78

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