8-6939089-C-T

Variant names:

• chr8-6939089-C-T
• rs45482601

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 0.0777 in 152,164 control chromosomes in the GnomAD database, including 512 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 0.078 (512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• 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 (NFE) allele frequency at 95% confidence interval = 0.0868 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: 0.0777 AC: 11820 AN: 152046 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0777 AC: 11818 AN: 152164 Hom.: 512 Cov.: 32 AF XY: 0.0759 AC XY: 5648 AN XY: 74368

African (AFR) AF: 0.0651 AC: 2705 AN: 41534

American (AMR) AF: 0.0833 AC: 1273 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0693 AC: 332 AN: 4790

European-Finnish (FIN) AF: 0.0527 AC: 559 AN: 10606

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0886 AC: 6026 AN: 67988

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.0693 Hom.: 284

Bravo AF: 0.0795

Asia WGS AF: 0.0370 AC: 128 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	4.9
DANN	Benign	0.36
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs45482601; hg19: chr8-6796611;