rs1954882

chr18-50764298-A-Gchr18-50764298-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;