3-168968888-C-T

Variant names:

• chr3-168968888-C-T
• rs16852912

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0806 in 152,030 control chromosomes in the GnomAD database, including 600 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 0.081 (600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 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: 0.0805 AC: 12223 AN: 151912 Hom.: 595 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0806 AC: 12248 AN: 152030 Hom.: 600 Cov.: 32 AF XY: 0.0781 AC XY: 5805 AN XY: 74308

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0691

Gnomad4 OTH AF: 0.0759

Alfa AF: 0.0623 Hom.: 297

Bravo AF: 0.0821

Asia WGS AF: 0.0600 AC: 208 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16852912; hg19: chr3-168686676;