rs3865186

Variant names:

• chr16-82613367-G-A
• rs3865186

Your query was ambiguous. Multiple possible variants found:

• chr16-82613367-G-A
• chr16-82613367-G-C
• chr16-82613367-G-T

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 0.761 in 152,128 control chromosomes in the GnomAD database, including 44,465 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 0.76 (44465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115615 AN: 152010 Hom.: 44423 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.761 AC: 115714 AN: 152128 Hom.: 44465 Cov.: 32 AF XY: 0.754 AC XY: 56073 AN XY: 74366

African (AFR) AF: 0.754 AC: 31289 AN: 41480

American (AMR) AF: 0.707 AC: 10808 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2188 AN: 5156

South Asian (SAS) AF: 0.709 AC: 3423 AN: 4826

European-Finnish (FIN) AF: 0.770 AC: 8151 AN: 10588

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54692 AN: 67998

Other (OTH) AF: 0.741 AC: 1569 AN: 2116

Alfa AF: 0.785 Hom.: 161942

Bravo AF: 0.754

Asia WGS AF: 0.573 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3865186; hg19: chr16-82646972;