8-49766589-C-T

Variant names:

• chr8-49766589-C-T
• rs4873375

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 0.664 in 152,036 control chromosomes in the GnomAD database, including 38,630 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 0.66 (38630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.665 AC: 100971 AN: 151918 Hom.: 38635 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.664 AC: 100976 AN: 152036 Hom.: 38630 Cov.: 32 AF XY: 0.670 AC XY: 49815 AN XY: 74322

African (AFR) AF: 0.253 AC: 10494 AN: 41456

American (AMR) AF: 0.739 AC: 11285 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2648 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4345 AN: 5144

South Asian (SAS) AF: 0.779 AC: 3751 AN: 4814

European-Finnish (FIN) AF: 0.865 AC: 9151 AN: 10582

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56863 AN: 67990

Other (OTH) AF: 0.677 AC: 1426 AN: 2106

Alfa AF: 0.724 Hom.: 5606

Bravo AF: 0.638

Asia WGS AF: 0.759 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.18
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4873375; hg19: chr8-50679149;