rs9878448

Variant names:

• chr3-30946248-C-T
• rs9878448

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 0.114 in 152,142 control chromosomes in the GnomAD database, including 2,792 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 0.11 (2792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.113 AC: 17217 AN: 152024 Hom.: 2774 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00279

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.114 AC: 17276 AN: 152142 Hom.: 2792 Cov.: 32 AF XY: 0.112 AC XY: 8351 AN XY: 74376

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.00279

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0439 Hom.: 258

Bravo AF: 0.130

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878448; hg19: chr3-30987740;