16-86481593-G-T

Variant names:

• chr16-86481593-G-T
• rs889593
• ENST00000595886.1:n.207-2837C>A

Variant summary

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

The ENST00000595886.1(FENDRR):​n.207-2837C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,146 control chromosomes in the GnomAD database, including 13,142 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 0.40 (13142 hom., cov: 33)
• Consequence: FENDRR ENST00000595886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 2 publications found

Genes affected

FENDRR (HGNC:43894): (FOXF1 adjacent non-coding developmental regulatory RNA) This gene produces a spliced long non-coding RNA transcribed bidirectionally with FOXF1 on the opposite strand. A similar gene in mouse is essential for normal development of the heart and body wall. The encoded transcript is thought to act by binding to polycomb repressive complex 2 (PRC2) and/or TrxG/MLL complexes to promote the methylation of the promoters of target genes, thus reducing their expression. It has been suggested that this transcript may play a role in the progression of gastric cancer. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595886.1. 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
	FENDRR	NR_033925.1		n.207-2837C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FENDRR	ENST00000595886.1	TSL:2	n.207-2837C>A		intron	N/A
	FENDRR	ENST00000600553.5	TSL:3	n.280-4394C>A		intron	N/A
	FENDRR	ENST00000659025.1		n.798-3461C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60309 AN: 152028 Hom.: 13152 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.396 AC: 60303 AN: 152146 Hom.: 13142 Cov.: 33 AF XY: 0.396 AC XY: 29483 AN XY: 74374

African (AFR) AF: 0.208 AC: 8631 AN: 41514

American (AMR) AF: 0.403 AC: 6166 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1441 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1999 AN: 5174

South Asian (SAS) AF: 0.402 AC: 1940 AN: 4822

European-Finnish (FIN) AF: 0.487 AC: 5150 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33532 AN: 67984

Other (OTH) AF: 0.426 AC: 898 AN: 2110

Alfa AF: 0.447 Hom.: 44751

Bravo AF: 0.382

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.52
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs889593; hg19: chr16-86515199;