chr8-116529369-T-C

Variant names:

• chr8-116529369-T-C
• rs13279799

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 0.144 in 152,114 control chromosomes in the GnomAD database, including 1,865 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 0.14 (1865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.144 AC: 21859 AN: 151996 Hom.: 1865 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.144 AC: 21858 AN: 152114 Hom.: 1865 Cov.: 32 AF XY: 0.147 AC XY: 10942 AN XY: 74332

African (AFR) AF: 0.0739 AC: 3069 AN: 41534

American (AMR) AF: 0.110 AC: 1687 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1717 AN: 5148

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4816

European-Finnish (FIN) AF: 0.212 AC: 2237 AN: 10560

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10693 AN: 67990

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.151 Hom.: 4478

Bravo AF: 0.134

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs13279799; hg19: chr8-117541607;