rs879500

Variant names:

• chr18-28544724-C-A
• rs879500

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 0.258 in 151,778 control chromosomes in the GnomAD database, including 5,249 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 0.26 (5249 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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: 0.258 AC: 39065 AN: 151660 Hom.: 5247 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.258 AC: 39085 AN: 151778 Hom.: 5249 Cov.: 31 AF XY: 0.257 AC XY: 19037 AN XY: 74188

African (AFR) AF: 0.256 AC: 10581 AN: 41404

American (AMR) AF: 0.237 AC: 3613 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1095 AN: 5144

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2591 AN: 10530

Middle Eastern (MID) AF: 0.203 AC: 59 AN: 290

European-Non Finnish (NFE) AF: 0.274 AC: 18595 AN: 67878

Other (OTH) AF: 0.245 AC: 515 AN: 2106

Alfa AF: 0.266 Hom.: 3740

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.62
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs879500; hg19: chr18-26124688;