rs9292019

Positions:

• chr5-53455194-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 0.0344 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;