8-59234530-C-T

Variant names:

• chr8-59234530-C-T
• rs12675886

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 0.451 in 151,876 control chromosomes in the GnomAD database, including 15,945 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 0.45 (15945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68471 AN: 151760 Hom.: 15923 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.451 AC: 68542 AN: 151876 Hom.: 15945 Cov.: 32 AF XY: 0.449 AC XY: 33285 AN XY: 74210

African (AFR) AF: 0.402 AC: 16666 AN: 41412

American (AMR) AF: 0.599 AC: 9141 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2756 AN: 5154

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3952 AN: 10510

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31203 AN: 67944

Other (OTH) AF: 0.501 AC: 1055 AN: 2104

Alfa AF: 0.442 Hom.: 1895

Bravo AF: 0.476

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12675886; hg19: chr8-60147089;