chr18-877771-A-G

Variant names:

• chr18-877771-A-G
• rs2846599

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 0.718 in 152,146 control chromosomes in the GnomAD database, including 41,771 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 0.72 (41771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 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: 0.718 AC: 109157 AN: 152028 Hom.: 41760 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.718 AC: 109210 AN: 152146 Hom.: 41771 Cov.: 32 AF XY: 0.716 AC XY: 53272 AN XY: 74378

African (AFR) AF: 0.426 AC: 17659 AN: 41492

American (AMR) AF: 0.790 AC: 12078 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2833 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4105 AN: 5172

South Asian (SAS) AF: 0.849 AC: 4095 AN: 4826

European-Finnish (FIN) AF: 0.756 AC: 8006 AN: 10584

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57877 AN: 67998

Other (OTH) AF: 0.738 AC: 1559 AN: 2112

Alfa AF: 0.764 Hom.: 6017

Bravo AF: 0.706

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	15
DANN	Benign	0.31
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2846599; hg19: chr18-877772;