chr3-101016787-T-C

Variant names:

• chr3-101016787-T-C
• rs9290276

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;