rs3909184

Positions:

• chr6-30731607-G-C
• chr6-30731607-G-T

Variant summary

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

The NM_005803.4(FLOT1):​c.724-507C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 151,300 control chromosomes in the GnomAD database, including 667 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 0.074 (667 hom., cov: 31)
• Consequence: FLOT1 NM_005803.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

FLOT1 (HGNC:3757): (flotillin 1) This gene encodes an protein that localizes to the caveolae, which are small domains on the inner cell membranes. This protein plays a role in vesicle trafficking and cell morphology. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

FLOT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLOT1	NM_005803.4	c.724-507C>G		intron_variant		ENST00000376389.8	NP_005794.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLOT1	ENST00000376389.8	c.724-507C>G		intron_variant		1	NM_005803.4	ENSP00000365569.3

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11223 AN: 151196 Hom.: 664 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0743 AC: 11238 AN: 151300 Hom.: 667 Cov.: 31 AF XY: 0.0740 AC XY: 5462 AN XY: 73854

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0816

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0114

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0455 Hom.: 34

Bravo AF: 0.0807

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.78

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: rs3909184; hg19: chr6-30699384;