chr8-127561053-A-G

Variant names:

• chr8-127561053-A-G
• rs12543106

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 0.272 in 152,108 control chromosomes in the GnomAD database, including 6,271 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 0.27 (6271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41254 AN: 151990 Hom.: 6250 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.272 AC: 41301 AN: 152108 Hom.: 6271 Cov.: 32 AF XY: 0.276 AC XY: 20500 AN XY: 74326

African (AFR) AF: 0.160 AC: 6652 AN: 41492

American (AMR) AF: 0.445 AC: 6809 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1378 AN: 5180

South Asian (SAS) AF: 0.319 AC: 1540 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3503 AN: 10560

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19676 AN: 67976

Other (OTH) AF: 0.283 AC: 595 AN: 2106

Alfa AF: 0.291 Hom.: 4264

Bravo AF: 0.270

Asia WGS AF: 0.314 AC: 1094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.8
DANN	Benign	0.61
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12543106; hg19: chr8-128573298;