8-116630189-C-T

Variant names:

• chr8-116630189-C-T
• rs28535528

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 0.184 in 152,030 control chromosomes in the GnomAD database, including 4,131 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 (4131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 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: 0.184 AC: 27929 AN: 151912 Hom.: 4124 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.184 AC: 27973 AN: 152030 Hom.: 4131 Cov.: 33 AF XY: 0.183 AC XY: 13606 AN XY: 74286

African (AFR) AF: 0.410 AC: 16984 AN: 41404

American (AMR) AF: 0.100 AC: 1531 AN: 15294

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

East Asian (EAS) AF: 0.0750 AC: 388 AN: 5174

South Asian (SAS) AF: 0.155 AC: 749 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1244 AN: 10548

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

European-Non Finnish (NFE) AF: 0.0885 AC: 6019 AN: 68000

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.146 Hom.: 325

Bravo AF: 0.190

Asia WGS AF: 0.149 AC: 519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs28535528; hg19: chr8-117642428;