16-89751681-A-G

Position:

• chr16-89751681-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000135.4(FANCA):​c.3066+457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,870 control chromosomes in the GnomAD database, including 23,223 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23223 hom., cov: 30)
• Consequence: FANCA NM_000135.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

Genes affected

FANCA (HGNC:3582): (FA complementation group A) 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 A. Alternative splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are the most common cause of Fanconi anemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FANCA	NM_000135.4	c.3066+457T>C		intron_variant		ENST00000389301.8
FANCA	NM_001286167.3	c.3066+457T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FANCA	ENST00000389301.8	c.3066+457T>C		intron_variant		1	NM_000135.4	P1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82062 AN: 151752 Hom.: 23189 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.472

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82150 AN: 151870 Hom.: 23223 Cov.: 30 AF XY: 0.549 AC XY: 40764 AN XY: 74214

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.477

Alfa AF: 0.493 Hom.: 17323

Bravo AF: 0.547

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	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

Other links and lift over

dbSNP: rs9926296; hg19: chr16-89818089;