rs9878516

Variant names:

• chr3-27740869-G-A
• rs9878516

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 0.0774 in 152,166 control chromosomes in the GnomAD database, including 512 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 0.077 (512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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: 0.0774 AC: 11764 AN: 152048 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0774 AC: 11771 AN: 152166 Hom.: 512 Cov.: 32 AF XY: 0.0778 AC XY: 5786 AN XY: 74388

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0449

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.0646

Alfa AF: 0.0629 Hom.: 459

Bravo AF: 0.0742

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.78
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878516; hg19: chr3-27782360;