rs2227019

Variant names:

• chr8-28757589-G-C
• rs2227019

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 0.227 in 151,954 control chromosomes in the GnomAD database, including 3,975 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 0.23 (3975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.227 AC: 34439 AN: 151836 Hom.: 3968 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.227 AC: 34451 AN: 151954 Hom.: 3975 Cov.: 32 AF XY: 0.226 AC XY: 16783 AN XY: 74256

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.235

Alfa AF: 0.216 Hom.: 455

Bravo AF: 0.229

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227019; hg19: chr8-28615106;