1-152418806-C-A

Position:

• chr1-152418806-C-A

Variant summary

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

The ENST00000411804.1(FLG-AS1):​n.95-26038C>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 0.59 in 151,952 control chromosomes in the GnomAD database, including 27,424 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 0.59 (27424 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000411804.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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.95-26038C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89548 AN: 151834 Hom.: 27404 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.590 AC: 89596 AN: 151952 Hom.: 27424 Cov.: 32 AF XY: 0.591 AC XY: 43870 AN XY: 74266

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.614

Alfa AF: 0.645 Hom.: 10182

Bravo AF: 0.567

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845766; hg19: chr1-152391282;