rs3811140

chr9-134880265-A-G

Variant summary

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

The XM_011518392.4(FCN2):c.68-2261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,098 control chromosomes in the GnomAD database, including 1,794 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 0.15 (1794 hom., cov: 32)
• Consequence: FCN2 XM_011518392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

FCN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCN2	XM_006717015.5	c.68-3037A>G		intron_variant
FCN2	XM_011518392.4	c.68-2261A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22055 AN: 151980 Hom.: 1783 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.145 AC: 22112 AN: 152098 Hom.: 1794 Cov.: 32 AF XY: 0.144 AC XY: 10683 AN XY: 74364

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0436

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.140

Alfa AF: 0.130 Hom.: 290

Bravo AF: 0.152

Asia WGS AF: 0.173 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.98
Dann	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3811140; hg19: chr9-137772111;