rs480752

Positions:

• chr1-181818649-C-A
• chr1-181818649-C-T

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 0.188 in 151,994 control chromosomes in the GnomAD database, including 2,939 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 0.19 (2939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28604 AN: 151876 Hom.: 2938 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.188 AC: 28608 AN: 151994 Hom.: 2939 Cov.: 32 AF XY: 0.188 AC XY: 13941 AN XY: 74298

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.193

Alfa AF: 0.169 Hom.: 2962

Bravo AF: 0.185

Asia WGS AF: 0.135 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.48
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs480752; hg19: chr1-181787784;