rs2243828

Variant names:

• chr17-58281523-A-G
• rs2243828

Your query was ambiguous. Multiple possible variants found:

• chr17-58281523-A-G
• chr17-58281523-A-T

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 0.239 in 151,992 control chromosomes in the GnomAD database, including 4,695 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 (4695 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.239 AC: 36252 AN: 151874 Hom.: 4686 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.239 AC: 36297 AN: 151992 Hom.: 4695 Cov.: 31 AF XY: 0.237 AC XY: 17624 AN XY: 74320

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.255

Alfa AF: 0.213 Hom.: 3916

Bravo AF: 0.247

Asia WGS AF: 0.128 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243828; hg19: chr17-56358884;