Variant 9-35077444-T-C 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 NM_004629.2(FANCG):c.511-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,612,430 control chromosomes in the GnomAD database, including 474,806 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.75 ( 43341 hom., cov: 29)

Exomes 𝑓: 0.77 ( 431465 hom. )

Consequence

FANCG
NM_004629.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.41

Variant links:

Genes affected

FANCG (HGNC:3588): (FA complementation group G) 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 G. [provided by RefSeq, Jul 2008]

FANCG links:

FANCG (HGNC:):

FANCG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 9-35077444-T-C is Benign according to our data. Variant chr9-35077444-T-C is described in ClinVar as [Benign]. Clinvar id is 259478.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FANCG	NM_004629.2 linkuse as main transcript	c.511-45A>G		intron_variant		ENST00000378643.8	NP_004620.1	O15287Q53XM5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FANCG	ENST00000378643.8 linkuse as main transcript	c.511-45A>G		intron_variant		1	NM_004629.2	ENSP00000367910.4		O15287

Frequencies

GnomAD3 genomes

AF:

0.753

AC:

114227

AN:

151754

Hom.:

43310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.741

Gnomad AMI

AF:

0.707

Gnomad AMR

AF:

0.794

Gnomad ASJ

AF:

0.796

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.718

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.751

GnomAD3 exomes

AF:

0.748

AC:

187783

AN:

251070

Hom.:

71422

AF XY:

0.746

AC XY:

101251

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.744

Gnomad AMR exome

AF:

0.844

Gnomad ASJ exome

AF:

0.791

Gnomad EAS exome

AF:

0.452

Gnomad SAS exome

AF:

0.709

Gnomad FIN exome

AF:

0.721

Gnomad NFE exome

AF:

0.778

Gnomad OTH exome

AF:

0.764

GnomAD4 exome

AF:

0.766

AC:

1119097

AN:

1460556

Hom.:

431465

Cov.:

AF XY:

0.765

AC XY:

556051

AN XY:

726678

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.841

Gnomad4 ASJ exome

AF:

0.791

Gnomad4 EAS exome

AF:

0.491

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.719

Gnomad4 NFE exome

AF:

0.780

Gnomad4 OTH exome

AF:

0.751

GnomAD4 genome

AF:

0.753

AC:

114310

AN:

151874

Hom.:

43341

Cov.:

AF XY:

0.749

AC XY:

55552

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.740

Gnomad4 AMR

AF:

0.795

Gnomad4 ASJ

AF:

0.796

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.718

Gnomad4 NFE

AF:

0.780

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.777

Hom.:

8477

Bravo

AF:

0.759

Asia WGS

AF:

0.583

AC:

2030

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Fanconi anemia complementation group G

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	Jul 01, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	- -

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

-0.95

CADD

Benign

0.71

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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