1-152415009-T-C

Position:

• chr1-152415009-T-C

Variant summary

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

The variant allele was found at a frequency of 0.811 in 152,146 control chromosomes in the GnomAD database, including 50,373 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 0.81 (50373 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.152415009T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLG-AS1	ENST00000411804.1	n.95-29835T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123299 AN: 152028 Hom.: 50337 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.811 AC: 123391 AN: 152146 Hom.: 50373 Cov.: 32 AF XY: 0.816 AC XY: 60740 AN XY: 74406

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.825

Alfa AF: 0.817 Hom.: 9134

Bravo AF: 0.807

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
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: rs4240877; hg19: chr1-152387485;