chr3-16174143-A-G

Variant names:

• chr3-16174143-A-G
• rs2102302

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 0.34 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.340 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

African (AFR) AF: 0.307 AC: 12692 AN: 41386

American (AMR) AF: 0.397 AC: 6067 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1480 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2454 AN: 5176

South Asian (SAS) AF: 0.539 AC: 2599 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2625 AN: 10588

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22556 AN: 67986

Other (OTH) AF: 0.359 AC: 757 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2102302; hg19: chr3-16215650;