16-84472761-C-G

Variant names:

• chr16-84472761-C-G
• rs400922

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 0.159 in 151,994 control chromosomes in the GnomAD database, including 2,440 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 0.16 (2440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 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: 0.159 AC: 24116 AN: 151876 Hom.: 2441 Cov.: 32

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.159 AC: 24117 AN: 151994 Hom.: 2440 Cov.: 32 AF XY: 0.165 AC XY: 12231 AN XY: 74294

African (AFR) AF: 0.0416 AC: 1724 AN: 41488

American (AMR) AF: 0.183 AC: 2791 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.0848 AC: 440 AN: 5186

South Asian (SAS) AF: 0.230 AC: 1104 AN: 4808

European-Finnish (FIN) AF: 0.275 AC: 2905 AN: 10548

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13961 AN: 67908

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.112 Hom.: 188

Bravo AF: 0.146

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.0
DANN	Benign	0.77
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs400922; hg19: chr16-84506367;