rs4846486

Positions:

• chr1-218532171-C-A

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 0.125 in 152,044 control chromosomes in the GnomAD database, including 1,402 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 0.13 (1402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.125 AC: 19020 AN: 151926 Hom.: 1400 Cov.: 32

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.125 AC: 19024 AN: 152044 Hom.: 1402 Cov.: 32 AF XY: 0.126 AC XY: 9341 AN XY: 74336

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.137

Alfa AF: 0.149 Hom.: 1073

Bravo AF: 0.124

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.85
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4846486; hg19: chr1-218705513;