rs3865186

Positions:

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

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 0.761 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.761 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

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.741

Alfa AF: 0.789 Hom.: 67481

Bravo AF: 0.754

Asia WGS AF: 0.573 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3865186; hg19: chr16-82646972;