rs1884008

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLRT2-AS1	ENST00000669085.2	n.2111C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000258945	ENST00000692489.2	n.326+1783G>A		intron_variant	Intron 1 of 1
FLRT2-AS1	ENST00000790578.1	n.1478+6758C>T		intron_variant	Intron 2 of 2

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 v4.3

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;