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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.705

Alfa AF: 0.642 Hom.: 17282

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1954882; hg19: chr18-48290668;