chr11-92367190-A-T

Variant names:

• chr11-92367190-A-T
• rs7129229
• NM_001367949.2:c.3292+11786A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAT3	NM_001367949.2	c.3292+11786A>T		intron_variant	Intron 2 of 27	ENST00000525166.6	NP_001354878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAT3	ENST00000525166.6	c.3292+11786A>T		intron_variant	Intron 2 of 27	5	NM_001367949.2	ENSP00000432586.2
PGAM1P9	ENST00000503887.1	n.61T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
FAT3	ENST00000409404.6	c.3292+11786A>T		intron_variant	Intron 1 of 24	5		ENSP00000387040.2
FAT3	ENST00000528921.1	n.219+11786A>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.503 AC: 2700 AN: 5368

American (AMR) AF: 0.129 AC: 1971 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 716 AN: 3226

East Asian (EAS) AF: 0.154 AC: 1525 AN: 9882

South Asian (SAS) AF: 0.168 AC: 4504 AN: 26860

European-Finnish (FIN) AF: 0.139 AC: 1045 AN: 7502

Middle Eastern (MID) AF: 0.212 AC: 113 AN: 534

European-Non Finnish (NFE) AF: 0.154 AC: 14228 AN: 92642

Other (OTH) AF: 0.167 AC: 1389 AN: 8314

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

African (AFR) AF: 0.499 AC: 20682 AN: 41452

American (AMR) AF: 0.176 AC: 2683 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.163 AC: 840 AN: 5156

South Asian (SAS) AF: 0.181 AC: 872 AN: 4812

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10586

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10855 AN: 67976

Other (OTH) AF: 0.224 AC: 470 AN: 2100

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
PhyloP100		3.6
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: rs7129229; hg19: chr11-92100356;