rs28909068

Variant names:

• chr9-134918662-T-C
• rs28909068

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0545 in 152,288 control chromosomes in the GnomAD database, including 262 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 0.054 (262 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0545 AC: 8290 AN: 152170 Hom.: 261 Cov.: 33

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0773

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0545 AC: 8296 AN: 152288 Hom.: 262 Cov.: 33 AF XY: 0.0551 AC XY: 4100 AN XY: 74446

African (AFR) AF: 0.0274 AC: 1137 AN: 41562

American (AMR) AF: 0.0365 AC: 559 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.0552 AC: 286 AN: 5182

South Asian (SAS) AF: 0.119 AC: 574 AN: 4832

European-Finnish (FIN) AF: 0.0773 AC: 820 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0695 AC: 4730 AN: 68014

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0634 Hom.: 147

Bravo AF: 0.0479

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.34
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs28909068; hg19: chr9-137810508;