dbSNP rs3126091: FLG-AS1:n.3387T>C (chr1-152334862-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658099.1(FLG-AS1):n.3387T>C 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 0.367 in 151,684 control chromosomes in the GnomAD database, including 14,474 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 0.37 ( 14474 hom., cov: 32)

Consequence

FLG-AS1
ENST00000658099.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.640

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CCDST	NR_103778.1 link	n.1081-477T>C	intron_variant	Intron 3 of 6
CCDST	NR_186761.1 link	n.744-477T>C	intron_variant	Intron 4 of 7
CCDST	NR_186762.1 link	n.346-477T>C	intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FLG-AS1	ENST00000658099.1 link	n.3387T>C	non_coding_transcript_exon_variant	Exon 1 of 4
FLG-AS1	ENST00000392688.7 link	n.1081-477T>C	intron_variant	Intron 3 of 6	2
FLG-AS1	ENST00000420707.5 link	n.681-477T>C	intron_variant	Intron 6 of 8	5

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55639

AN:

151566

Hom.:

14432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.699

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.367

AC:

55729

AN:

151684

Hom.:

14474

Cov.:

AF XY:

0.373

AC XY:

27664

AN XY:

74118

show subpopulations

Gnomad4 AFR

AF:

0.699

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.444

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.274

Hom.:

1441

Bravo

AF:

0.399

Asia WGS

AF:

0.575

AC:

1998

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.8

DANN

Benign

0.71

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