chr5-151506958-A-G

Position:

• chr5-151506958-A-G

Variant summary

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

The NM_001447.3(FAT2):​c.12517+196T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,164 control chromosomes in the GnomAD database, including 33,007 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 0.63 (33007 hom., cov: 33)
• Consequence: FAT2 NM_001447.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

FAT2 (HGNC:3596): (FAT atypical cadherin 2) This gene is the second identified human homolog 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 two epidermal growth factor (EGF)-like repeats and one laminin G domain. This protein most likely functions as a cell adhesion molecule, controlling cell proliferation and playing an important role in cerebellum development. [provided by RefSeq, Jul 2008]

SLC36A1 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAT2	NM_001447.3	c.12517+196T>C		intron_variant		ENST00000261800.6	NP_001438.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAT2	ENST00000261800.6	c.12517+196T>C		intron_variant		1	NM_001447.3	ENSP00000261800	P1
FAT2	ENST00000520200.5	c.2834+196T>C		intron_variant		1		ENSP00000429678

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95820 AN: 152046 Hom.: 33005 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.630 AC: 95854 AN: 152164 Hom.: 33007 Cov.: 33 AF XY: 0.638 AC XY: 47418 AN XY: 74378

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.651

Alfa AF: 0.659 Hom.: 4330

Bravo AF: 0.616

Asia WGS AF: 0.798 AC: 2777 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	1.6
DANN	Benign	0.44

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: rs7722485; hg19: chr5-150886519; COSMIC: COSV55816004; COSMIC: COSV55816004;