rs4846486

Variant names:

• chr1-218532171-C-A
• rs4846486

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0426 AC: 1766 AN: 41476

American (AMR) AF: 0.135 AC: 2066 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1034 AN: 5154

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10584

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10593 AN: 67968

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.139 Hom.: 1695

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4846486; hg19: chr1-218705513;