rs9878516

chr3-27740869-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;