8-5068943-C-T

Variant names:

• chr8-5068943-C-T
• rs1454292

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 0.619 in 151,580 control chromosomes in the GnomAD database, including 29,503 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 0.62 (29503 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.618 AC: 93658 AN: 151460 Hom.: 29446 Cov.: 29

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.619 AC: 93777 AN: 151580 Hom.: 29503 Cov.: 29 AF XY: 0.616 AC XY: 45649 AN XY: 74076

African (AFR) AF: 0.743 AC: 30706 AN: 41326

American (AMR) AF: 0.605 AC: 9193 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2239 AN: 3462

East Asian (EAS) AF: 0.597 AC: 3040 AN: 5096

South Asian (SAS) AF: 0.495 AC: 2378 AN: 4800

European-Finnish (FIN) AF: 0.596 AC: 6272 AN: 10528

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.562 AC: 38144 AN: 67876

Other (OTH) AF: 0.582 AC: 1225 AN: 2106

Alfa AF: 0.579 Hom.: 45721

Bravo AF: 0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.52
DANN	Benign	0.53
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1454292; hg19: chr8-4926465;