rs528846

Variant names:

• chr1-182623201-C-T
• rs528846

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 0.169 in 152,008 control chromosomes in the GnomAD database, including 3,104 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 0.17 (3104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25587 AN: 151890 Hom.: 3087 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.169 AC: 25644 AN: 152008 Hom.: 3104 Cov.: 32 AF XY: 0.166 AC XY: 12309 AN XY: 74264

African (AFR) AF: 0.346 AC: 14355 AN: 41432

American (AMR) AF: 0.0926 AC: 1415 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3472

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5172

South Asian (SAS) AF: 0.0580 AC: 279 AN: 4808

European-Finnish (FIN) AF: 0.127 AC: 1337 AN: 10544

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7312 AN: 67978

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.121 Hom.: 2949

Bravo AF: 0.174

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.59
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs528846; hg19: chr1-182592336; COSMIC: COSV59995903;