11-92709293-C-T

Variant summary

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

The NM_001367949.2(FAT3):c.3669+11848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,272 control chromosomes in the GnomAD database, including 242 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 0.037 (242 hom., cov: 33)
• Consequence: FAT3 NM_001367949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAT3	NM_001367949.2	c.3669+11848C>T		intron_variant		ENST00000525166.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAT3	ENST00000525166.6	c.3669+11848C>T		intron_variant		5	NM_001367949.2
FAT3	ENST00000409404.6	c.3669+11848C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5577 AN: 152154 Hom.: 242 Cov.: 33

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0178

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00919

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0367 AC: 5581 AN: 152272 Hom.: 242 Cov.: 33 AF XY: 0.0399 AC XY: 2973 AN XY: 74446

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.0473

Gnomad4 NFE AF: 0.00920

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.00751 Hom.: 1

Bravo AF: 0.0338

Asia WGS AF: 0.117 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.0
Dann	Benign	0.83

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: rs10501794; hg19: chr11-92442459;