Variant rs10205 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004475.3(FLOT2):c.*459C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,007,476 control chromosomes in the GnomAD database, including 54,182 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 0.41 ( 15859 hom., cov: 32)

Exomes 𝑓: 0.29 ( 38323 hom. )

Consequence

FLOT2
NM_004475.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.969

Variant links:

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]

FLOT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLOT2	NM_004475.3 linkuse as main transcript	c.*459C>T		3_prime_UTR_variant	11/11	ENST00000394908.9	NP_004466.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLOT2	ENST00000394908.9 linkuse as main transcript	c.*459C>T		3_prime_UTR_variant	11/11	1	NM_004475.3	ENSP00000378368	P3

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62184

AN:

151960

Hom.:

15813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.380

GnomAD4 exome

AF:

0.292

AC:

249525

AN:

855398

Hom.:

38323

Cov.:

AF XY:

0.290

AC XY:

114983

AN XY:

396734

show subpopulations

Gnomad4 AFR exome

AF:

0.766

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.262

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.257

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.283

Gnomad4 OTH exome

AF:

0.298

GnomAD4 genome

AF:

0.410

AC:

62280

AN:

152078

Hom.:

15859

Cov.:

AF XY:

0.406

AC XY:

30157

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.731

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.370

Hom.:

1983

Bravo

AF:

0.419

Asia WGS

AF:

0.247

AC:

859

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.48

DANN

Benign

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over