rs16861194

Positions:

• chr3-186841636-A-G

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 0.15 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0685

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.0829

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0931 Hom.: 351

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16861194; hg19: chr3-186559425;