rs16861194

Variant names:

• chr3-186841636-A-G
• rs16861194

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 0.15 in 152,078 control chromosomes in the GnomAD database, including 2,187 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 0.15 (2187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.40
• Publications: 75 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.150 AC: 22790 AN: 151960 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.150 AC: 22830 AN: 152078 Hom.: 2187 Cov.: 32 AF XY: 0.157 AC XY: 11678 AN XY: 74328

African (AFR) AF: 0.245 AC: 10141 AN: 41438

American (AMR) AF: 0.163 AC: 2491 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3470

East Asian (EAS) AF: 0.185 AC: 955 AN: 5174

South Asian (SAS) AF: 0.0685 AC: 330 AN: 4818

European-Finnish (FIN) AF: 0.253 AC: 2675 AN: 10582

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5636 AN: 68014

Other (OTH) AF: 0.124 AC: 262 AN: 2110

Alfa AF: 0.103 Hom.: 1902

Bravo AF: 0.146

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.72
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs16861194; hg19: chr3-186559425;