rs12664111

Variant names:

• chr6-139818678-A-G
• rs12664111
• ENST00000642381.1:n.252-38086A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642381.1(FILNC1):​n.252-38086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,228 control chromosomes in the GnomAD database, including 1,095 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 0.099 (1095 hom., cov: 32)
• Consequence: FILNC1 ENST00000642381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 6 publications found

Genes affected

FILNC1 (HGNC:53755): (FOXO induced long non-coding RNA 1) This gene produces a long non-coding RNA that is induced by forkhead box O proteins and plays a role in stress-induced apoptosis. Knock down of transcripts at this locus results in increased renal tumor growth and alteration in genes involved in glucose metabolism. This RNA interacts with heterogeneous nuclear ribonucleoprotein D and prevents it from binding to Myc mRNA, therefore suppressing Myc activity. Alternative splicing and transcriptional start site usage results in multiple transcript variants. [provided by RefSeq, Oct 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FILNC1	NR_038399.2	n.52-38086A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FILNC1	ENST00000642381.1	n.252-38086A>G		intron_variant	Intron 2 of 3
FILNC1	ENST00000644936.1	n.204-38086A>G		intron_variant	Intron 1 of 2
FILNC1	ENST00000647189.1	n.255-38086A>G		intron_variant	Intron 2 of 3
FILNC1	ENST00000647420.1	n.208-38086A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15038 AN: 152110 Hom.: 1088 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0989 AC: 15060 AN: 152228 Hom.: 1095 Cov.: 32 AF XY: 0.101 AC XY: 7520 AN XY: 74436

African (AFR) AF: 0.0240 AC: 997 AN: 41562

American (AMR) AF: 0.171 AC: 2616 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1660 AN: 5158

South Asian (SAS) AF: 0.166 AC: 799 AN: 4822

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10594

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7211 AN: 68014

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.104 Hom.: 1038

Bravo AF: 0.100

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs12664111; hg19: chr6-140139815;