rs3120665

chr1-152344114-A-G

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+2904A>G 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 0.264 in 151,922 control chromosomes in the GnomAD database, including 6,640 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 0.26 (6640 hom., cov: 32)
• Consequence: FLG-AS1 NR_103778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLG-AS1	NR_103778.1	n.1406+2904A>G		intron_variant, non_coding_transcript_variant
FLG-AS1	NR_103779.1	n.151+2904A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLG-AS1	ENST00000653548.1	n.757+6025A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40027 AN: 151804 Hom.: 6618 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40082 AN: 151922 Hom.: 6640 Cov.: 32 AF XY: 0.268 AC XY: 19889 AN XY: 74264

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.264

Alfa AF: 0.183 Hom.: 3552

Bravo AF: 0.285

Asia WGS AF: 0.413 AC: 1434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.45
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3120665; hg19: chr1-152316590;