chr8-116630751-C-T

Variant names:

• chr8-116630751-C-T
• rs16888611

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.179 in 152,218 control chromosomes in the GnomAD database, including 3,829 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 0.18 (3829 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.179 AC: 27222 AN: 152100 Hom.: 3822 Cov.: 34

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.179 AC: 27260 AN: 152218 Hom.: 3829 Cov.: 34 AF XY: 0.178 AC XY: 13261 AN XY: 74416

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0751

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.155

Alfa AF: 0.0803 Hom.: 188

Bravo AF: 0.184

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16888611; hg19: chr8-117642990;