rs6469653

Variant names:

• chr8-116619725-G-A
• rs6469653

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 0.454 in 151,284 control chromosomes in the GnomAD database, including 18,048 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 0.45 (18048 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.454 AC: 68602 AN: 151186 Hom.: 18055 Cov.: 30

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.454 AC: 68618 AN: 151284 Hom.: 18048 Cov.: 30 AF XY: 0.452 AC XY: 33383 AN XY: 73814

African (AFR) AF: 0.201 AC: 8296 AN: 41218

American (AMR) AF: 0.445 AC: 6760 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1617 AN: 3466

East Asian (EAS) AF: 0.177 AC: 898 AN: 5068

South Asian (SAS) AF: 0.503 AC: 2412 AN: 4798

European-Finnish (FIN) AF: 0.578 AC: 5974 AN: 10340

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40841 AN: 67886

Other (OTH) AF: 0.497 AC: 1045 AN: 2102

Alfa AF: 0.545 Hom.: 70305

Bravo AF: 0.432

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.82
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs6469653; hg19: chr8-117631964;