chr1-152417976-T-C

Variant names:

• chr1-152417976-T-C
• rs941934
• ENST00000411804.1:n.95-26868T>C

Variant summary

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

The ENST00000411804.1(FLG-AS1):​n.95-26868T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,052 control chromosomes in the GnomAD database, including 65,931 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 0.93 (65931 hom., cov: 29)
• Consequence: FLG-AS1 ENST00000411804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

FLG-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.95-26868T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141367 AN: 151934 Hom.: 65871 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.931 AC: 141486 AN: 152052 Hom.: 65931 Cov.: 29 AF XY: 0.933 AC XY: 69325 AN XY: 74300

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.938

Alfa AF: 0.904 Hom.: 26550

Bravo AF: 0.935

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941934; hg19: chr1-152390452;