rs6892289

Variant names:

• chr5-82775094-A-G
• rs6892289

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 0.135 in 152,226 control chromosomes in the GnomAD database, including 1,521 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 0.14 (1521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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 (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.135 AC: 20569 AN: 152108 Hom.: 1522 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.135 AC: 20581 AN: 152226 Hom.: 1521 Cov.: 33 AF XY: 0.131 AC XY: 9760 AN XY: 74432

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0612

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.168

Alfa AF: 0.142 Hom.: 2217

Bravo AF: 0.142

Asia WGS AF: 0.0990 AC: 343 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	2.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6892289; hg19: chr5-82070913;