rs1679666

chr8-108527618-C-Achr8-108527618-C-T

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 0.161 in 152,094 control chromosomes in the GnomAD database, including 2,523 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 (2523 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24498 AN: 151976 Hom.: 2521 Cov.: 33

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.161 AC: 24496 AN: 152094 Hom.: 2523 Cov.: 33 AF XY: 0.164 AC XY: 12229 AN XY: 74378

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.146

Alfa AF: 0.173 Hom.: 1456

Bravo AF: 0.160

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.8
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1679666; hg19: chr8-109539847;