rs1876486

Variant names:

• chr18-75090996-A-G
• rs1876486

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 0.882 in 152,290 control chromosomes in the GnomAD database, including 59,609 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 0.88 (59609 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.882 AC: 134203 AN: 152172 Hom.: 59563 Cov.: 34

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.882 AC: 134309 AN: 152290 Hom.: 59609 Cov.: 34 AF XY: 0.877 AC XY: 65303 AN XY: 74460

African (AFR) AF: 0.807 AC: 33533 AN: 41542

American (AMR) AF: 0.921 AC: 14097 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3250 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3454 AN: 5182

South Asian (SAS) AF: 0.926 AC: 4471 AN: 4828

European-Finnish (FIN) AF: 0.853 AC: 9038 AN: 10598

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63469 AN: 68036

Other (OTH) AF: 0.892 AC: 1888 AN: 2116

Alfa AF: 0.918 Hom.: 51047

Bravo AF: 0.882

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1876486; hg19: chr18-72802952;