rs9816383

Variant names:

• chr3-14777314-G-A
• rs9816383

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.419 AC: 17347 AN: 41438

American (AMR) AF: 0.200 AC: 3059 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.0372 AC: 193 AN: 5184

South Asian (SAS) AF: 0.151 AC: 730 AN: 4820

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10592

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8641 AN: 67998

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.185 Hom.: 5495

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
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs9816383; hg19: chr3-14818821;