rs4545169

Variant names:

• chr9-134890095-T-G
• rs4545169

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 0.165 in 152,156 control chromosomes in the GnomAD database, including 2,581 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 0.17 (2581 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.165 AC: 25118 AN: 152038 Hom.: 2578 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0969

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.165 AC: 25156 AN: 152156 Hom.: 2581 Cov.: 33 AF XY: 0.163 AC XY: 12105 AN XY: 74366

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0969

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.153

Alfa AF: 0.169 Hom.: 388

Bravo AF: 0.175

Asia WGS AF: 0.160 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4545169; hg19: chr9-137781941;