rs28670272

Variant names:

• chr15-67817569-A-G
• rs28670272

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 0.304 in 151,446 control chromosomes in the GnomAD database, including 8,119 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 0.30 (8119 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

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 (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.303 AC: 45922 AN: 151330 Hom.: 8085 Cov.: 29

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.304 AC: 46008 AN: 151446 Hom.: 8119 Cov.: 29 AF XY: 0.304 AC XY: 22473 AN XY: 74002

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.314

Alfa AF: 0.272 Hom.: 1621

Bravo AF: 0.334

Asia WGS AF: 0.496 AC: 1723 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	5.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28670272; hg19: chr15-68109907;