rs2082804

Variant names:

• chr8-63248328-G-A
• rs2082804

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 0.156 in 151,948 control chromosomes in the GnomAD database, including 2,431 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 0.16 (2431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.156 AC: 23727 AN: 151830 Hom.: 2422 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.156 AC: 23767 AN: 151948 Hom.: 2431 Cov.: 32 AF XY: 0.156 AC XY: 11589 AN XY: 74252

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0959

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.151

Alfa AF: 0.105 Hom.: 532

Bravo AF: 0.166

Asia WGS AF: 0.227 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2082804; hg19: chr8-64160886;