1-152328745-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000392688.7(FLG-AS1):​n.915-3838A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 151,918 control chromosomes in the GnomAD database, including 66,648 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 0.94 ( 66648 hom., cov: 31)

Consequence

FLG-AS1
ENST00000392688.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.296
Variant links:
Genes affected
CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDSTNR_103778.1 linkn.915-3838A>G intron_variant Intron 2 of 6
CCDSTNR_186761.1 linkn.578-3838A>G intron_variant Intron 3 of 7
CCDSTNR_186762.1 linkn.180-3838A>G intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FLG-AS1ENST00000392688.7 linkn.915-3838A>G intron_variant Intron 2 of 6 2
FLG-AS1ENST00000420707.5 linkn.515-3838A>G intron_variant Intron 5 of 8 5
FLG-AS1ENST00000593011.5 linkn.429-3838A>G intron_variant Intron 3 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.935
AC:
142001
AN:
151800
Hom.:
66588
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.986
Gnomad AMI
AF:
0.939
Gnomad AMR
AF:
0.949
Gnomad ASJ
AF:
0.951
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.978
Gnomad FIN
AF:
0.826
Gnomad MID
AF:
0.949
Gnomad NFE
AF:
0.909
Gnomad OTH
AF:
0.950
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.936
AC:
142120
AN:
151918
Hom.:
66648
Cov.:
31
AF XY:
0.934
AC XY:
69350
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.986
Gnomad4 AMR
AF:
0.949
Gnomad4 ASJ
AF:
0.951
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.978
Gnomad4 FIN
AF:
0.826
Gnomad4 NFE
AF:
0.909
Gnomad4 OTH
AF:
0.951
Alfa
AF:
0.923
Hom.:
7505
Bravo
AF:
0.948
Asia WGS
AF:
0.988
AC:
3437
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
10
DANN
Benign
0.84

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1933063; hg19: chr1-152301221; API