rs16892766

Variant names:

• chr8-116618444-A-C
• rs16892766

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0913 in 152,184 control chromosomes in the GnomAD database, including 752 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 0.091 (752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.26
• Publications: 188 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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: 0.0914 AC: 13895 AN: 152066 Hom.: 751 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.000583

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0913 AC: 13900 AN: 152184 Hom.: 752 Cov.: 32 AF XY: 0.0924 AC XY: 6870 AN XY: 74390

African (AFR) AF: 0.127 AC: 5274 AN: 41550

American (AMR) AF: 0.0591 AC: 903 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3466

East Asian (EAS) AF: 0.000584 AC: 3 AN: 5134

South Asian (SAS) AF: 0.0898 AC: 433 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10594

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5280 AN: 68012

Other (OTH) AF: 0.0884 AC: 187 AN: 2116

Alfa AF: 0.0797 Hom.: 2551

Bravo AF: 0.0879

Asia WGS AF: 0.0460 AC: 161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Benign	0.75
PhyloP100		4.3

Splicing

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

Other links and lift over

dbSNP: rs16892766; hg19: chr8-117630683; COSMIC: COSV58902220;