rs3097779

Variant names:

• chr5-151560146-A-C
• rs3097779
• NM_001447.3:c.3574+3179T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-151560146-A-C
• chr5-151560146-A-T

Variant summary

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

The NM_001447.3(FAT2):​c.3574+3179T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,016 control chromosomes in the GnomAD database, including 32,535 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 0.65 (32535 hom., cov: 32)
• Consequence: FAT2 NM_001447.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 2 publications found

Genes affected

FAT2 (HGNC:3596): (FAT atypical cadherin 2) This gene is the second identified human homolog of the Drosophila fat gene, which encodes a tumor suppressor essential for controlling cell proliferation during Drosophila development. The gene product is a member of the cadherin superfamily, a group of integral membrane proteins characterized by the presence of cadherin-type repeats. In addition to containing 34 tandem cadherin-type repeats, the gene product has two epidermal growth factor (EGF)-like repeats and one laminin G domain. This protein most likely functions as a cell adhesion molecule, controlling cell proliferation and playing an important role in cerebellum development. [provided by RefSeq, Jul 2008]

FAT2 Gene-Disease associations (from GenCC):

• spinocerebellar ataxia 45

  Inheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Illumina, Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001447.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAT2	NM_001447.3	MANE Select	c.3574+3179T>G		intron	N/A	NP_001438.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAT2	ENST00000261800.6	TSL:1 MANE Select	c.3574+3179T>G		intron	N/A	ENSP00000261800.5

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99126 AN: 151900 Hom.: 32491 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.653 AC: 99223 AN: 152016 Hom.: 32535 Cov.: 32 AF XY: 0.651 AC XY: 48419 AN XY: 74348

African (AFR) AF: 0.625 AC: 25912 AN: 41450

American (AMR) AF: 0.720 AC: 11005 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3466

East Asian (EAS) AF: 0.659 AC: 3399 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4814

European-Finnish (FIN) AF: 0.668 AC: 7060 AN: 10572

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44927 AN: 67966

Other (OTH) AF: 0.662 AC: 1394 AN: 2106

Alfa AF: 0.671 Hom.: 23182

Bravo AF: 0.663

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.64
PhyloP100		0.47
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: rs3097779; hg19: chr5-150939707;