rs9878208

Variant names:

• chr3-185638388-T-G
• rs9878208

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 0.0852 in 152,174 control chromosomes in the GnomAD database, including 810 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 0.085 (810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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 (SAS) allele frequency at 95% confidence interval = 0.315 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: 0.0852 AC: 12953 AN: 152056 Hom.: 814 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0852 AC: 12960 AN: 152174 Hom.: 810 Cov.: 32 AF XY: 0.0886 AC XY: 6589 AN XY: 74394

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.0883

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0602 Hom.: 337

Bravo AF: 0.0813

Asia WGS AF: 0.253 AC: 880 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	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9878208; hg19: chr3-185356176;