rs1679666

Variant names:

• chr8-108527618-C-A
• rs1679666

Your query was ambiguous. Multiple possible variants found:

• chr8-108527618-C-A
• chr8-108527618-C-T

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 0.161 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0571 AC: 2369 AN: 41508

American (AMR) AF: 0.242 AC: 3698 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2266 AN: 5162

South Asian (SAS) AF: 0.142 AC: 681 AN: 4812

European-Finnish (FIN) AF: 0.202 AC: 2142 AN: 10580

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12410 AN: 67986

Other (OTH) AF: 0.146 AC: 308 AN: 2116

Alfa AF: 0.177 Hom.: 2143

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1679666; hg19: chr8-109539847;