rs9292019

Variant names:

• chr5-53455194-T-C
• rs9292019

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 0.0344 in 152,236 control chromosomes in the GnomAD database, including 115 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 0.034 (115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0818 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: 0.0344 AC: 5230 AN: 152118 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.0382

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0344 AC: 5239 AN: 152236 Hom.: 115 Cov.: 32 AF XY: 0.0349 AC XY: 2595 AN XY: 74436

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.0232

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.0885

Gnomad4 SAS AF: 0.0376

Gnomad4 FIN AF: 0.0338

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0317 Hom.: 11

Bravo AF: 0.0329

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292019; hg19: chr5-52751024;