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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

5 publications found
Variant links:
Genes affected
FLRT2-AS1 (HGNC:55912): (FLRT2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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-AS1ENST00000669085.2 linkn.1653-2243C>A intron_variant Intron 2 of 2
ENSG00000258945ENST00000692489.2 linkn.326+4484G>T intron_variant Intron 1 of 1
FLRT2-AS1ENST00000790578.1 linkn.1478+4057C>A intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.512
AC:
77675
AN:
151812
Hom.:
20321
Cov.:
32
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1911
3823
5734
7646
9557
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
696
1392
2088
2784
3480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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

Publications

Other links and lift over

dbSNP: rs1884009; hg19: chr14-85987605; API