rs1933064

Positions:

• chr1-152329100-G-A
• chr1-152329100-G-C
• chr1-152329100-G-T

Variant summary

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

The NR_103778.1(FLG-AS1):​n.915-3483G>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 0.578 in 151,712 control chromosomes in the GnomAD database, including 27,208 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 0.58 (27208 hom., cov: 32)
• Consequence: FLG-AS1 NR_103778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758

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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLG-AS1	NR_103778.1	n.915-3483G>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.390-3483G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87616 AN: 151594 Hom.: 27159 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.578 AC: 87725 AN: 151712 Hom.: 27208 Cov.: 32 AF XY: 0.578 AC XY: 42857 AN XY: 74146

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.564

Alfa AF: 0.491 Hom.: 19114

Bravo AF: 0.604

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933064; hg19: chr1-152301576;