rs16854884

Variant names:

• chr3-144059866-A-C
• rs16854884

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 0.285 in 152,136 control chromosomes in the GnomAD database, including 6,413 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 0.28 (6413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 8 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 = 0.365 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: 0.285 AC: 43307 AN: 152018 Hom.: 6396 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.285 AC: 43354 AN: 152136 Hom.: 6413 Cov.: 33 AF XY: 0.285 AC XY: 21170 AN XY: 74366

African (AFR) AF: 0.370 AC: 15353 AN: 41492

American (AMR) AF: 0.235 AC: 3589 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5180

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4818

European-Finnish (FIN) AF: 0.280 AC: 2959 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17597 AN: 67986

Other (OTH) AF: 0.283 AC: 597 AN: 2110

Alfa AF: 0.270 Hom.: 15626

Bravo AF: 0.285

Asia WGS AF: 0.197 AC: 686 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	3.3
DANN	Benign	0.45
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs16854884; hg19: chr3-143778708;