1-152407652-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000411804.1(FLG-AS1):n.94+33605C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,028 control chromosomes in the GnomAD database, including 2,734 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 0.17 (2734 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: FLG-AS1 ENST00000411804.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

FLG-AS1 (HGNC:27913): (cervical cancer associated DHX9 suppressive transcript)

ACMG classification

Verdict is Benign. Variant got -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 = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLG-AS1	ENST00000411804.1	n.94+33605C>T		intron_variant, non_coding_transcript_variant		3
FLG-AS1	ENST00000628475.2	n.167-102C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26165 AN: 151894 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.172 AC: 26177 AN: 152012 Hom.: 2734 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74284

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.190

Alfa AF: 0.133 Hom.: 595

Bravo AF: 0.182

Asia WGS AF: 0.338 AC: 1174 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	2.1
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923509; hg19: chr1-152380128;