ENST00000669085.2:n.1653-2243C>A

Variant names:

• chr14-85521261-G-T
• rs1884009
• ENST00000669085.2:n.1653-2243C>A

Variant summary

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

The ENST00000669085.2(FLRT2-AS1):​n.1653-2243C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,930 control chromosomes in the GnomAD database, including 20,346 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 (20346 hom., cov: 32)
• Consequence: FLRT2-AS1 ENST00000669085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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.1653-2243C>A		intron_variant	Intron 2 of 2
ENSG00000258945	ENST00000692489.2	n.326+4484G>T		intron_variant	Intron 1 of 1
FLRT2-AS1	ENST00000790578.1	n.1478+4057C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77675 AN: 151812 Hom.: 20321 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.512 AC: 77742 AN: 151930 Hom.: 20346 Cov.: 32 AF XY: 0.513 AC XY: 38084 AN XY: 74254

African (AFR) AF: 0.458 AC: 18954 AN: 41404

American (AMR) AF: 0.537 AC: 8211 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4283 AN: 5148

South Asian (SAS) AF: 0.551 AC: 2656 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4683 AN: 10554

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35311 AN: 67936

Other (OTH) AF: 0.529 AC: 1118 AN: 2114

Alfa AF: 0.518 Hom.: 10072

Bravo AF: 0.519

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1884009; hg19: chr14-85987605;