rs10489884

Positions:

• chr1-152345145-G-A

Variant summary

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

The NR_103778.1(FLG-AS1):​n.1406+3935G>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 0.0961 in 151,966 control chromosomes in the GnomAD database, including 1,754 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 0.096 (1754 hom., cov: 32)
• Consequence: FLG-AS1 NR_103778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLG-AS1	NR_103778.1	n.1406+3935G>A		intron_variant, non_coding_transcript_variant
FLG-AS1	NR_103779.1	n.151+3935G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000653548.1	n.757+7056G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14581 AN: 151848 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.00783

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0961 AC: 14606 AN: 151966 Hom.: 1754 Cov.: 32 AF XY: 0.0934 AC XY: 6936 AN XY: 74280

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.00870

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.00783

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0646

Alfa AF: 0.0515 Hom.: 217

Bravo AF: 0.107

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489884; hg19: chr1-152317621;