8-5687469-T-C

Position:

• chr8-5687469-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.177

Alfa AF: 0.164 Hom.: 1046

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7817815; hg19: chr8-5544991;