rs1884008

chr14-85518560-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLRT2-AS1	ENST00000669085.2	n.2111C>T		non_coding_transcript_exon_variant	3/3
	ENST00000692489.1	n.247+1783G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.556

Alfa AF: 0.505 Hom.: 39616

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884008; hg19: chr14-85984904;