rs4545169

chr9-134890095-T-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 0.165 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/exons	MANE	UniProt

Ensembl

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