8-5687469-T-C

Variant names:

• chr8-5687469-T-C
• rs7817815

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 0.165 in 152,082 control chromosomes in the GnomAD database, including 2,161 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 0.16 (2161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 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: 0.165 AC: 25058 AN: 151964 Hom.: 2160 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.165 AC: 25062 AN: 152082 Hom.: 2161 Cov.: 33 AF XY: 0.161 AC XY: 11976 AN XY: 74316

African (AFR) AF: 0.156 AC: 6485 AN: 41514

American (AMR) AF: 0.141 AC: 2158 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.0400 AC: 206 AN: 5156

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4816

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10594

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12684 AN: 67954

Other (OTH) AF: 0.177 AC: 373 AN: 2112

Alfa AF: 0.165 Hom.: 1188

Bravo AF: 0.167

Asia WGS AF: 0.129 AC: 447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs7817815; hg19: chr8-5544991;