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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;