rs1820489

Variant names:

• chr15-48392904-C-T
• rs1820489

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 0.783 in 152,142 control chromosomes in the GnomAD database, including 48,565 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 0.78 (48565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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 (NFE) allele frequency at 95% confidence interval = 0.897 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: 0.784 AC: 119121 AN: 152024 Hom.: 48567 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.783 AC: 119152 AN: 152142 Hom.: 48565 Cov.: 31 AF XY: 0.781 AC XY: 58072 AN XY: 74386

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.812

Alfa AF: 0.836 Hom.: 12273

Bravo AF: 0.774

Asia WGS AF: 0.568 AC: 1979 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	0.74
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820489; hg19: chr15-48685101;