rs6892289

Positions:

• chr5-82775094-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;