rs3816848

chr17-28881571-G-A

Variant summary

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

The NM_004475.3(FLOT2):c.915-196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,178 control chromosomes in the GnomAD database, including 28,014 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 0.57 (28014 hom., cov: 34)
• Consequence: FLOT2 NM_004475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

Genes affected

FLOT2 (HGNC:3758): (flotillin 2) Caveolae are small domains on the inner cell membrane involved in vesicular trafficking and signal transduction. This gene encodes a caveolae-associated, integral membrane protein, which is thought to function in neuronal signaling. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLOT2	NM_004475.3	c.915-196C>T		intron_variant		ENST00000394908.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLOT2	ENST00000394908.9	c.915-196C>T		intron_variant		1	NM_004475.3	P3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87301 AN: 152060 Hom.: 28008 Cov.: 34

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.574 AC: 87321 AN: 152178 Hom.: 28014 Cov.: 34 AF XY: 0.576 AC XY: 42827 AN XY: 74390

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.611

Alfa AF: 0.673 Hom.: 15107

Bravo AF: 0.558

Asia WGS AF: 0.714 AC: 2483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.7
Dann	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs3816848; hg19: chr17-27208589;