6-1339954-C-T

Variant names:

• chr6-1339954-C-T
• rs9502893
• ENST00000721686.1:n.90-15027G>A

Variant summary

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

The ENST00000721686.1(LINC01394):​n.90-15027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,062 control chromosomes in the GnomAD database, including 20,129 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 0.51 (20129 hom., cov: 32)
• Consequence: LINC01394 ENST00000721686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 29 publications found

Genes affected

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

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721686.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXF2-DT	NR_187218.1		n.444-15027G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01394	ENST00000721686.1		n.90-15027G>A		intron	N/A
	LINC01394	ENST00000721687.1		n.277-15027G>A		intron	N/A
	LINC01394	ENST00000721688.1		n.347-15027G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77496 AN: 151946 Hom.: 20122 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.510 AC: 77520 AN: 152062 Hom.: 20129 Cov.: 32 AF XY: 0.509 AC XY: 37806 AN XY: 74296

African (AFR) AF: 0.426 AC: 17653 AN: 41476

American (AMR) AF: 0.439 AC: 6714 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3098 AN: 5172

South Asian (SAS) AF: 0.493 AC: 2374 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5620 AN: 10552

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38220 AN: 67978

Other (OTH) AF: 0.506 AC: 1069 AN: 2112

Alfa AF: 0.545 Hom.: 101335

Bravo AF: 0.499

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs9502893; hg19: chr6-1340189; COSMIC: COSV50192851;