3-16174143-A-G

Variant names:

• chr3-16174143-A-G
• rs2102302

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 0.34 in 152,036 control chromosomes in the GnomAD database, including 9,069 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 0.34 (9069 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 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: 0.340 AC: 51713 AN: 151918 Hom.: 9060 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.340 AC: 51750 AN: 152036 Hom.: 9069 Cov.: 33 AF XY: 0.342 AC XY: 25392 AN XY: 74322

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.359

Alfa AF: 0.341 Hom.: 1576

Bravo AF: 0.347

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102302; hg19: chr3-16215650;