Genetic Variant FLG-AS1:n.915-3838A>G (chr1-152328745-A-G) – ACMG Classification: Benign (-12 pts)

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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.296

Variant links:

Genes affected

FLG-AS1 (HGNC:):

FLG-AS1 links:

CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

CCDST links:

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	Effect	Exon rank
CCDST	NR_103778.1 link	n.915-3838A>G	intron_variant	Intron 2 of 6
CCDST	NR_186761.1 link	n.578-3838A>G	intron_variant	Intron 3 of 7
CCDST	NR_186762.1 link	n.180-3838A>G	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FLG-AS1	ENST00000392688.7 link	n.915-3838A>G	intron_variant	Intron 2 of 6	2
FLG-AS1	ENST00000420707.5 link	n.515-3838A>G	intron_variant	Intron 5 of 8	5
FLG-AS1	ENST00000593011.5 link	n.429-3838A>G	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.935

AC:

142001

AN:

151800

Hom.:

66588

Cov.:

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.:

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over