rs2166842

Variant names:

• chr8-567596-A-C
• rs2166842

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 0.205 in 152,174 control chromosomes in the GnomAD database, including 3,581 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 0.20 (3581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.205 AC: 31123 AN: 152056 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.205 AC: 31191 AN: 152174 Hom.: 3581 Cov.: 32 AF XY: 0.204 AC XY: 15150 AN XY: 74400

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.192

Alfa AF: 0.163 Hom.: 3457

Bravo AF: 0.216

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2166842; hg19: chr8-517596;