Variant rs7865453 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XM_011518392.4(FCN2):c.68-1768A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,296,572 control chromosomes in the GnomAD database, including 8,725 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 0.14 ( 1638 hom., cov: 33)

Exomes 𝑓: 0.11 ( 7087 hom. )

Consequence

FCN2
XM_011518392.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0930

Variant links:

Genes affected

FCN2 (HGNC:):

FCN2 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCN2	XM_006717015.5 linkuse as main transcript	c.68-2544A>C		intron_variant
FCN2	XM_011518392.4 linkuse as main transcript	c.68-1768A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20728

AN:

152100

Hom.:

1629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0427

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0900

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.134

GnomAD4 exome

AF:

0.106

AC:

121503

AN:

1144354

Hom.:

7087

AF XY:

0.106

AC XY:

61319

AN XY:

581090

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.0489

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.114

Gnomad4 FIN exome

AF:

0.0999

Gnomad4 NFE exome

AF:

0.0998

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.137

AC:

20782

AN:

152218

Hom.:

1638

Cov.:

AF XY:

0.134

AC XY:

10008

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.220

Gnomad4 AMR

AF:

0.123

Gnomad4 ASJ

AF:

0.0427

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0900

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.0749

Hom.:

Bravo

AF:

0.145

Asia WGS

AF:

0.150

AC:

527

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.2

DANN

Benign

0.52

Splicing

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