chr8-5017650-G-T

Variant names:

• chr8-5017650-G-T
• rs10112481

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 0.652 in 152,070 control chromosomes in the GnomAD database, including 32,928 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 0.65 (32928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 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: 0.652 AC: 99133 AN: 151952 Hom.: 32896 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.652 AC: 99216 AN: 152070 Hom.: 32928 Cov.: 32 AF XY: 0.646 AC XY: 47995 AN XY: 74328

African (AFR) AF: 0.745 AC: 30918 AN: 41492

American (AMR) AF: 0.522 AC: 7979 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2402 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2964 AN: 5154

South Asian (SAS) AF: 0.760 AC: 3661 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5544 AN: 10568

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43445 AN: 67954

Other (OTH) AF: 0.674 AC: 1425 AN: 2114

Alfa AF: 0.643 Hom.: 120751

Bravo AF: 0.653

Asia WGS AF: 0.655 AC: 2279 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	0.031
DANN	Benign	0.45
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs10112481; hg19: chr8-4875172;