rs16892766

Positions:

• chr8-116618444-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.000584

Gnomad4 SAS AF: 0.0898

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.0884

Alfa AF: 0.0774 Hom.: 1138

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

Splicing

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

Publications

LitVar

Other links and lift over

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