rs16828327

Variant names:

• chr3-157796877-C-T
• rs16828327

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 0.207 in 152,112 control chromosomes in the GnomAD database, including 3,326 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 (3326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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: 0.207 AC: 31448 AN: 151996 Hom.: 3312 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.207 AC: 31499 AN: 152112 Hom.: 3326 Cov.: 32 AF XY: 0.211 AC XY: 15698 AN XY: 74356

African (AFR) AF: 0.226 AC: 9361 AN: 41480

American (AMR) AF: 0.255 AC: 3899 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5176

South Asian (SAS) AF: 0.181 AC: 874 AN: 4826

European-Finnish (FIN) AF: 0.222 AC: 2344 AN: 10562

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12855 AN: 68004

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.192 Hom.: 5577

Bravo AF: 0.213

Asia WGS AF: 0.217 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs16828327; hg19: chr3-157514666;