3-168955544-G-A

Variant names:

• chr3-168955544-G-A
• rs16852880

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0400 AC: 1661 AN: 41554

American (AMR) AF: 0.201 AC: 3074 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1588 AN: 5164

South Asian (SAS) AF: 0.0563 AC: 272 AN: 4832

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0257 AC: 1745 AN: 68016

Other (OTH) AF: 0.0673 AC: 142 AN: 2110

Alfa AF: 0.0388 Hom.: 163

Bravo AF: 0.0740

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Benign	0.59
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs16852880; hg19: chr3-168673332;