rs2304865

chr4-186604209-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005245.4(FAT1):c.10548+168G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,010 control chromosomes in the GnomAD database, including 6,683 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (6683 hom., cov: 32)
• Consequence: FAT1 NM_005245.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.17

Genes affected

FAT1 (HGNC:3595): (FAT atypical cadherin 1) This gene is an ortholog 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 five epidermal growth factor (EGF)-like repeats and one laminin A-G domain. This gene is expressed at high levels in a number of fetal epithelia. Its product probably functions as an adhesion molecule and/or signaling receptor, and is likely to be important in developmental processes and cell communication. Transcript variants derived from alternative splicing and/or alternative promoter usage exist, but they have not been fully described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 4-186604209-C-G is Benign according to our data. Variant chr4-186604209-C-G is described in ClinVar as [Benign]. Clinvar id is 1225803.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAT1	NM_005245.4	c.10548+168G>C		intron_variant		ENST00000441802.7
FAT1	XM_005262834.4	c.10548+168G>C		intron_variant
FAT1	XM_005262835.3	c.10548+168G>C		intron_variant
FAT1	XM_006714139.4	c.10548+168G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAT1	ENST00000441802.7	c.10548+168G>C		intron_variant		5	NM_005245.4	P1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43235 AN: 151890 Hom.: 6682 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.284 AC: 43235 AN: 152010 Hom.: 6683 Cov.: 32 AF XY: 0.286 AC XY: 21239 AN XY: 74282

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.312

Alfa AF: 0.299 Hom.: 887

Bravo AF: 0.288

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.015
Dann	Benign	0.49

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: rs2304865; hg19: chr4-187525363;