rs28611189

Variant names:

• chr8-42665191-T-C
• rs28611189

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 0.208 in 152,192 control chromosomes in the GnomAD database, including 3,800 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 0.21 (3800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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: 0.208 AC: 31643 AN: 152074 Hom.: 3801 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31649 AN: 152192 Hom.: 3800 Cov.: 32 AF XY: 0.206 AC XY: 15305 AN XY: 74424

African (AFR) AF: 0.331 AC: 13755 AN: 41508

American (AMR) AF: 0.147 AC: 2247 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.0789 AC: 409 AN: 5182

South Asian (SAS) AF: 0.184 AC: 886 AN: 4828

European-Finnish (FIN) AF: 0.191 AC: 2024 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11028 AN: 68008

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.187 Hom.: 1439

Bravo AF: 0.209

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.48
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs28611189; hg19: chr8-42520334;