rs6862233

Variant names:

• chr5-80105467-A-G
• rs6862233

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 0.332 in 151,736 control chromosomes in the GnomAD database, including 9,196 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 0.33 (9196 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.332 AC: 50293 AN: 151618 Hom.: 9186 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.332 AC: 50335 AN: 151736 Hom.: 9196 Cov.: 30 AF XY: 0.328 AC XY: 24296 AN XY: 74132

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.322

Alfa AF: 0.284 Hom.: 3494

Bravo AF: 0.343

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6862233; hg19: chr5-79401290;