5-86306799-G-T

Variant names:

• chr5-86306799-G-T
• rs10070239

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 0.791 in 152,068 control chromosomes in the GnomAD database, including 49,477 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 0.79 (49477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.791 AC: 120183 AN: 151950 Hom.: 49465 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.791 AC: 120238 AN: 152068 Hom.: 49477 Cov.: 31 AF XY: 0.787 AC XY: 58490 AN XY: 74344

African (AFR) AF: 0.548 AC: 22724 AN: 41438

American (AMR) AF: 0.737 AC: 11264 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2966 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4291 AN: 5162

South Asian (SAS) AF: 0.811 AC: 3899 AN: 4810

European-Finnish (FIN) AF: 0.886 AC: 9389 AN: 10592

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.926 AC: 62962 AN: 67996

Other (OTH) AF: 0.807 AC: 1707 AN: 2114

Alfa AF: 0.789 Hom.: 4343

Bravo AF: 0.768

Asia WGS AF: 0.799 AC: 2775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
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: rs10070239; hg19: chr5-85602617;