rs9878448

Positions:

• chr3-30946248-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;