8-116630751-C-T

Variant names:

• chr8-116630751-C-T
• rs16888611

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 0.179 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.393 AC: 16318 AN: 41488

American (AMR) AF: 0.0984 AC: 1505 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3472

East Asian (EAS) AF: 0.0751 AC: 389 AN: 5178

South Asian (SAS) AF: 0.151 AC: 727 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1250 AN: 10616

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0886 AC: 6024 AN: 68026

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.0949 Hom.: 613

Bravo AF: 0.184

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs16888611; hg19: chr8-117642990;