rs3124953

Positions:

• chr9-134880220-A-G
• chr9-134880220-A-T

Variant summary

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

The XM_011518392.4(FCN2):​c.68-2306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,204 control chromosomes in the GnomAD database, including 54,780 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 0.85 (54780 hom., cov: 31)
• Consequence: FCN2 XM_011518392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

FCN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCN2	XM_006717015.5	c.68-3082A>G		intron_variant			XP_006717078.1
FCN2	XM_011518392.4	c.68-2306A>G		intron_variant			XP_011516694.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128499 AN: 152086 Hom.: 54721 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.845 AC: 128619 AN: 152204 Hom.: 54780 Cov.: 31 AF XY: 0.845 AC XY: 62894 AN XY: 74410

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.826

Alfa AF: 0.792 Hom.: 7499

Bravo AF: 0.848

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124953; hg19: chr9-137772066;