rs1954882

Variant names:

• chr18-50764298-A-G
• rs1954882

Your query was ambiguous. Multiple possible variants found:

• chr18-50764298-A-G
• chr18-50764298-A-T

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 0.703 in 152,088 control chromosomes in the GnomAD database, including 38,363 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 0.70 (38363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.703 AC: 106870 AN: 151970 Hom.: 38309 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.703 AC: 106980 AN: 152088 Hom.: 38363 Cov.: 32 AF XY: 0.708 AC XY: 52668 AN XY: 74356

African (AFR) AF: 0.827 AC: 34299 AN: 41498

American (AMR) AF: 0.761 AC: 11631 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2392 AN: 3464

East Asian (EAS) AF: 0.868 AC: 4499 AN: 5184

South Asian (SAS) AF: 0.759 AC: 3666 AN: 4828

European-Finnish (FIN) AF: 0.641 AC: 6753 AN: 10542

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41472 AN: 67974

Other (OTH) AF: 0.705 AC: 1489 AN: 2112

Alfa AF: 0.643 Hom.: 23512

Bravo AF: 0.719

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.89
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1954882; hg19: chr18-48290668;