rs3865185

Variant names:

• chr16-82612857-T-A
• rs3865185

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 0.776 in 152,152 control chromosomes in the GnomAD database, including 46,293 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 0.78 (46293 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 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: 0.776 AC: 117908 AN: 152034 Hom.: 46254 Cov.: 33

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.776 AC: 118004 AN: 152152 Hom.: 46293 Cov.: 33 AF XY: 0.769 AC XY: 57171 AN XY: 74374

African (AFR) AF: 0.758 AC: 31467 AN: 41502

American (AMR) AF: 0.722 AC: 11036 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2181 AN: 5152

South Asian (SAS) AF: 0.742 AC: 3576 AN: 4820

European-Finnish (FIN) AF: 0.781 AC: 8270 AN: 10594

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56224 AN: 68012

Other (OTH) AF: 0.763 AC: 1609 AN: 2108

Alfa AF: 0.805 Hom.: 6160

Bravo AF: 0.768

Asia WGS AF: 0.583 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs3865185; hg19: chr16-82646462;