14-85518560-G-A

Variant names:

• chr14-85518560-G-A
• rs1884008
• ENST00000669085.2:n.2111C>T

Variant summary

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

The ENST00000669085.2(FLRT2-AS1):​n.2111C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,974 control chromosomes in the GnomAD database, including 24,026 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 0.55 (24026 hom., cov: 32)
• Consequence: FLRT2-AS1 ENST00000669085.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 5 publications found

Genes affected

FLRT2-AS1 (HGNC:55912): (FLRT2 antisense RNA 1)

ENSG00000258945 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669085.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLRT2-AS1	ENST00000669085.2		n.2111C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000258945	ENST00000692489.2		n.326+1783G>A		intron	N/A
	FLRT2-AS1	ENST00000790578.1		n.1478+6758C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84053 AN: 151856 Hom.: 23977 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.554 AC: 84159 AN: 151974 Hom.: 24026 Cov.: 32 AF XY: 0.554 AC XY: 41172 AN XY: 74280

African (AFR) AF: 0.687 AC: 28460 AN: 41444

American (AMR) AF: 0.523 AC: 7993 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1760 AN: 3462

East Asian (EAS) AF: 0.677 AC: 3497 AN: 5164

South Asian (SAS) AF: 0.562 AC: 2712 AN: 4826

European-Finnish (FIN) AF: 0.426 AC: 4489 AN: 10542

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33410 AN: 67946

Other (OTH) AF: 0.556 AC: 1173 AN: 2108

Alfa AF: 0.513 Hom.: 85945

Bravo AF: 0.562

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1884008; hg19: chr14-85984904;