rs28909068

chr9-134918662-T-C

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 0.0545 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0365

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0552

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0773

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0640 Hom.: 81

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28909068; hg19: chr9-137810508;