chr1-152301540-G-A

Position:

• chr1-152301540-G-A

Variant summary

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

The ENST00000653548.1(FLG-AS1):​n.390-31043G>A 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 0.187 in 152,072 control chromosomes in the GnomAD database, including 3,795 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 0.19 (3795 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000653548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 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	ENST00000653548.1	n.390-31043G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28363 AN: 151954 Hom.: 3788 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.187 AC: 28376 AN: 152072 Hom.: 3795 Cov.: 32 AF XY: 0.198 AC XY: 14747 AN XY: 74338

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.219

Alfa AF: 0.158 Hom.: 310

Bravo AF: 0.196

Asia WGS AF: 0.501 AC: 1738 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	4.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12730241; hg19: chr1-152274016;