rs3785161

Variant names:

• chr16-55759783-A-C
• rs3785161

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 152,176 control chromosomes in the GnomAD database, including 1,919 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 (1919 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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: 22865 AN: 152058 Hom.: 1916 Cov.: 33

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.150 AC: 22876 AN: 152176 Hom.: 1919 Cov.: 33 AF XY: 0.153 AC XY: 11359 AN XY: 74380

African (AFR) AF: 0.0666 AC: 2766 AN: 41542

American (AMR) AF: 0.188 AC: 2872 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1330 AN: 5162

South Asian (SAS) AF: 0.158 AC: 760 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1735 AN: 10600

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12413 AN: 67978

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.171 Hom.: 4104

Bravo AF: 0.147

Asia WGS AF: 0.181 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.41
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3785161; hg19: chr16-55793695;