rs16852880

chr3-168955544-G-Achr3-168955544-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.057 in 152,256 control chromosomes in the GnomAD database, including 723 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 0.057 (723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8671 AN: 152138 Hom.: 717 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0570 AC: 8683 AN: 152256 Hom.: 723 Cov.: 32 AF XY: 0.0602 AC XY: 4480 AN XY: 74448

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.0563

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0673

Alfa AF: 0.0397 Hom.: 157

Bravo AF: 0.0740

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	17
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16852880; hg19: chr3-168673332;