ENST00000721686.1:n.90-12149C>T

Variant names:

• chr6-1337076-G-A
• rs11242679
• ENST00000721686.1:n.90-12149C>T

Variant summary

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

The ENST00000721686.1(LINC01394):​n.90-12149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,500 control chromosomes in the GnomAD database, including 1,991 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 (1991 hom., cov: 32)
• Consequence: LINC01394 ENST00000721686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 4 publications found

Genes affected

LINC01394 (HGNC:50670): (long intergenic non-protein coding RNA 1394)

ENSG00000294194 (HGNC:):

FOXF2-DT (HGNC:50662): (FOXF2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2-DT	NR_187218.1	n.444-12149C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01394	ENST00000721686.1	n.90-12149C>T		intron_variant	Intron 1 of 2
LINC01394	ENST00000721687.1	n.277-12149C>T		intron_variant	Intron 2 of 3
LINC01394	ENST00000721688.1	n.347-12149C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22845 AN: 151384 Hom.: 1989 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.151 AC: 22868 AN: 151500 Hom.: 1991 Cov.: 32 AF XY: 0.158 AC XY: 11690 AN XY: 73966

African (AFR) AF: 0.166 AC: 6865 AN: 41278

American (AMR) AF: 0.212 AC: 3228 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1813 AN: 5148

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4808

European-Finnish (FIN) AF: 0.150 AC: 1555 AN: 10390

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7770 AN: 67904

Other (OTH) AF: 0.122 AC: 257 AN: 2104

Alfa AF: 0.122 Hom.: 2874

Bravo AF: 0.155

Asia WGS AF: 0.262 AC: 910 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	0.12
DANN	Benign	0.75
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs11242679; hg19: chr6-1337311;