chr1-152286602-A-G

Position:

• chr1-152286602-A-G

Variant summary

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

The ENST00000653548.1(FLG-AS1):​n.389+34844A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.156 in 152,102 control chromosomes in the GnomAD database, including 3,088 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 0.16 (3088 hom., cov: 32)
• Consequence: FLG-AS1 ENST00000653548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000653548.1	n.389+34844A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23726 AN: 151984 Hom.: 3085 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.156 AC: 23725 AN: 152102 Hom.: 3088 Cov.: 32 AF XY: 0.168 AC XY: 12457 AN XY: 74366

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.191

Alfa AF: 0.156 Hom.: 2986

Bravo AF: 0.165

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11204971; hg19: chr1-152259078;