rs9816383

Variant names:

• chr3-14777314-G-A
• rs9816383

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 0.212 in 152,118 control chromosomes in the GnomAD database, including 4,789 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 0.21 (4789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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: 0.212 AC: 32222 AN: 152000 Hom.: 4784 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.212 AC: 32258 AN: 152118 Hom.: 4789 Cov.: 33 AF XY: 0.210 AC XY: 15594 AN XY: 74356

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.210

Alfa AF: 0.152 Hom.: 1911

Bravo AF: 0.227

Asia WGS AF: 0.113 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9816383; hg19: chr3-14818821;