rs9290276

Positions:

• chr3-101016787-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 0.277 in 152,030 control chromosomes in the GnomAD database, including 6,312 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 0.28 (6312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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 = 0.423 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: 0.277 AC: 42103 AN: 151912 Hom.: 6292 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.277 AC: 42155 AN: 152030 Hom.: 6312 Cov.: 32 AF XY: 0.283 AC XY: 21038 AN XY: 74314

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.263

Alfa AF: 0.278 Hom.: 2856

Bravo AF: 0.273

Asia WGS AF: 0.365 AC: 1269 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	4.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290276; hg19: chr3-100735631;