chr8-116628076-C-T

Variant names:

• chr8-116628076-C-T
• rs11986063

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 0.121 in 151,892 control chromosomes in the GnomAD database, including 1,322 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 0.12 (1322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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: 0.121 AC: 18400 AN: 151774 Hom.: 1323 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.121 AC: 18417 AN: 151892 Hom.: 1322 Cov.: 31 AF XY: 0.123 AC XY: 9103 AN XY: 74234

African (AFR) AF: 0.191 AC: 7926 AN: 41390

American (AMR) AF: 0.0739 AC: 1129 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3468

East Asian (EAS) AF: 0.0720 AC: 372 AN: 5166

South Asian (SAS) AF: 0.138 AC: 665 AN: 4814

European-Finnish (FIN) AF: 0.119 AC: 1252 AN: 10516

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6094 AN: 67956

Other (OTH) AF: 0.111 AC: 234 AN: 2108

Alfa AF: 0.0975 Hom.: 1752

Bravo AF: 0.119

Asia WGS AF: 0.129 AC: 449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.57
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs11986063; hg19: chr8-117640315;