rs10501797

chr11-92794804-C-G

Variant summary

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

The NM_001367949.2(FAT3):c.4822+1827C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,016 control chromosomes in the GnomAD database, including 8,748 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 0.33 (8748 hom., cov: 32)
• Consequence: FAT3 NM_001367949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

FAT3 (HGNC:23112): (FAT atypical cadherin 3) Predicted to enable calcium ion binding activity. Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within several processes, including negative regulation of dendrite development; neuron migration; and retina layer formation. Predicted to be located in dendrite and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAT3	NM_001367949.2	c.4822+1827C>G		intron_variant		ENST00000525166.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAT3	ENST00000525166.6	c.4822+1827C>G		intron_variant		5	NM_001367949.2
FAT3	ENST00000409404.6	c.4822+1827C>G		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50646 AN: 151898 Hom.: 8744 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.333 AC: 50681 AN: 152016 Hom.: 8748 Cov.: 32 AF XY: 0.329 AC XY: 24473 AN XY: 74282

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.331

Alfa AF: 0.339 Hom.: 1084

Bravo AF: 0.334

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.51

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: rs10501797; hg19: chr11-92527970;