rs28670272

Positions:

• chr15-67817569-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;