8-69897026-T-C

Variant names:

• chr8-69897026-T-C
• rs12680109

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 0.391 in 152,050 control chromosomes in the GnomAD database, including 11,821 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 0.39 (11821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.391 AC: 59410 AN: 151934 Hom.: 11826 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.391 AC: 59429 AN: 152050 Hom.: 11821 Cov.: 32 AF XY: 0.395 AC XY: 29338 AN XY: 74310

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.403

Alfa AF: 0.399 Hom.: 16120

Bravo AF: 0.390

Asia WGS AF: 0.496 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12680109; hg19: chr8-70809261;