rs228269

Variant names:

• chr17-38833557-G-A
• rs228269

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 0.244 in 152,052 control chromosomes in the GnomAD database, including 4,618 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 0.24 (4618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.295 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: 0.244 AC: 37112 AN: 151934 Hom.: 4618 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.244 AC: 37139 AN: 152052 Hom.: 4618 Cov.: 32 AF XY: 0.240 AC XY: 17850 AN XY: 74314

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.247

Alfa AF: 0.236 Hom.: 578

Bravo AF: 0.254

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.26
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228269; hg19: chr17-36989810;