chr8-26051983-C-T

Variant names:

• chr8-26051983-C-T
• rs4872389

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 0.243 in 152,138 control chromosomes in the GnomAD database, including 4,731 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 0.24 (4731 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.243 AC: 37016 AN: 152020 Hom.: 4728 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.243 AC: 37033 AN: 152138 Hom.: 4731 Cov.: 33 AF XY: 0.247 AC XY: 18367 AN XY: 74386

African (AFR) AF: 0.229 AC: 9518 AN: 41496

American (AMR) AF: 0.302 AC: 4621 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 706 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1827 AN: 5142

South Asian (SAS) AF: 0.199 AC: 960 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2980 AN: 10592

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15660 AN: 68002

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.237 Hom.: 1470

Bravo AF: 0.247

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4872389; hg19: chr8-25909499;