rs2873892

Variant names:

• chr8-139234730-G-A
• rs2873892

Your query was ambiguous. Multiple possible variants found:

• chr8-139234730-G-A
• chr8-139234730-G-C
• chr8-139234730-G-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 0.242 in 151,900 control chromosomes in the GnomAD database, including 4,997 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 0.24 (4997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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: 0.242 AC: 36718 AN: 151782 Hom.: 4988 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.242 AC: 36736 AN: 151900 Hom.: 4997 Cov.: 32 AF XY: 0.246 AC XY: 18236 AN XY: 74222

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.228

Alfa AF: 0.139 Hom.: 267

Bravo AF: 0.243

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2873892; hg19: chr8-140246973;