1-152407652-C-T

Variant names:

• chr1-152407652-C-T
• rs1923509
• ENST00000411804.1:n.94+33605C>T

Variant summary

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

The ENST00000411804.1(FLG-AS1):​n.94+33605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,028 control chromosomes in the GnomAD database, including 2,734 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 0.17 (2734 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: FLG-AS1 ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

FLG-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000411804.1	n.94+33605C>T		intron_variant	Intron 1 of 1	3
FLG-AS1	ENST00000628475.2	n.167-102C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26165 AN: 151894 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.172 AC: 26177 AN: 152012 Hom.: 2734 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74284

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.190

Alfa AF: 0.133 Hom.: 595

Bravo AF: 0.182

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923509; hg19: chr1-152380128;