15-85827510-C-T

Variant names:

• chr15-85827510-C-T
• rs7166323

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.69 (28658 hom., cov: 16)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.692 AC: 81029 AN: 117040 Hom.: 28628 Cov.: 16

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.692 AC: 81103 AN: 117130 Hom.: 28658 Cov.: 16 AF XY: 0.687 AC XY: 37794 AN XY: 55018

African (AFR) AF: 0.865 AC: 26474 AN: 30612

American (AMR) AF: 0.735 AC: 7490 AN: 10188

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2103 AN: 3070

East Asian (EAS) AF: 0.655 AC: 2685 AN: 4102

South Asian (SAS) AF: 0.684 AC: 2299 AN: 3360

European-Finnish (FIN) AF: 0.492 AC: 2648 AN: 5378

Middle Eastern (MID) AF: 0.780 AC: 184 AN: 236

European-Non Finnish (NFE) AF: 0.614 AC: 35479 AN: 57822

Other (OTH) AF: 0.697 AC: 1114 AN: 1598

Alfa AF: 0.523 Hom.: 1117

Bravo AF: 0.734

Asia WGS AF: 0.660 AC: 2275 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7166323; hg19: chr15-86370741;