rs7129229

Positions:

• chr11-92367190-A-T

Variant summary

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

The NM_001367949.2(FAT3):​c.3292+11786A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 321,610 control chromosomes in the GnomAD database, including 9,642 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 0.25 (6748 hom., cov: 32)
  • Exomes 𝑓: 0.17 (2894 hom.)
• Consequence: FAT3 NM_001367949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.58

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]

PGAM1P9 (HGNC:42456): (phosphoglycerate mutase 1 pseudogene 9)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAT3	NM_001367949.2	c.3292+11786A>T		intron_variant		ENST00000525166.6	NP_001354878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAT3	ENST00000525166.6	c.3292+11786A>T		intron_variant		5	NM_001367949.2	ENSP00000432586
PGAM1P9	ENST00000503887.1	n.61T>A		non_coding_transcript_exon_variant	1/1
FAT3	ENST00000409404.6	c.3292+11786A>T		intron_variant		5		ENSP00000387040	P1
FAT3	ENST00000528921.1	n.219+11786A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38666 AN: 151908 Hom.: 6725 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.166 AC: 28191 AN: 169584 Hom.: 2894 Cov.: 0 AF XY: 0.166 AC XY: 15457 AN XY: 93208

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.168

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.154

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.255 AC: 38735 AN: 152026 Hom.: 6748 Cov.: 32 AF XY: 0.251 AC XY: 18665 AN XY: 74316

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.224

Alfa AF: 0.217 Hom.: 589

Bravo AF: 0.268

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	2.9
DANN	Benign	0.77

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: rs7129229; hg19: chr11-92100356;