3-10031627-C-A

Variant names:

• chr3-10031627-C-A
• rs7648104
• NM_001018115.3:c.65-1205C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001018115.3(FANCD2):​c.65-1205C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,768 control chromosomes in the GnomAD database, including 3,463 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 0.20 (3463 hom., cov: 31)
• Consequence: FANCD2 NM_001018115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 11 publications found

Genes affected

FANCD2 (HGNC:3585): (FA complementation group D2) 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 D2. This protein is monoubiquinated in response to DNA damage, resulting in its localization to nuclear foci with other proteins (BRCA1 AND BRCA2) involved in homology-directed DNA repair. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

FANCD2 Gene-Disease associations (from GenCC):

• Fanconi anemia complementation group D2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001018115.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FANCD2	NM_001018115.3	MANE Select	c.65-1205C>A		intron	N/A	NP_001018125.1
	FANCD2	NM_033084.6		c.65-1205C>A		intron	N/A	NP_149075.2
	FANCD2	NM_001374254.1		c.65-1205C>A		intron	N/A	NP_001361183.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FANCD2	ENST00000675286.1	MANE Select	c.65-1205C>A		intron	N/A	ENSP00000502379.1
	FANCD2	ENST00000287647.7	TSL:1	c.65-1205C>A		intron	N/A	ENSP00000287647.3
	FANCD2	ENST00000419585.5	TSL:1	c.65-1205C>A		intron	N/A	ENSP00000398754.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29944 AN: 151652 Hom.: 3459 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.197 AC: 29969 AN: 151768 Hom.: 3463 Cov.: 31 AF XY: 0.192 AC XY: 14251 AN XY: 74158

African (AFR) AF: 0.320 AC: 13253 AN: 41400

American (AMR) AF: 0.145 AC: 2212 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3466

East Asian (EAS) AF: 0.0654 AC: 338 AN: 5172

South Asian (SAS) AF: 0.162 AC: 780 AN: 4812

European-Finnish (FIN) AF: 0.117 AC: 1225 AN: 10468

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10993 AN: 67916

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.118 Hom.: 252

Bravo AF: 0.207

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7648104; hg19: chr3-10073311;