6-88008048-A-G

Variant names:

• chr6-88008048-A-G
• rs366676

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 0.455 in 151,992 control chromosomes in the GnomAD database, including 16,361 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 (16361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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: 0.455 AC: 69090 AN: 151874 Hom.: 16360 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.455 AC: 69109 AN: 151992 Hom.: 16361 Cov.: 32 AF XY: 0.464 AC XY: 34450 AN XY: 74282

African (AFR) AF: 0.365 AC: 15126 AN: 41448

American (AMR) AF: 0.514 AC: 7847 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1607 AN: 3468

East Asian (EAS) AF: 0.771 AC: 3985 AN: 5170

South Asian (SAS) AF: 0.525 AC: 2527 AN: 4810

European-Finnish (FIN) AF: 0.576 AC: 6075 AN: 10552

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30539 AN: 67962

Other (OTH) AF: 0.445 AC: 936 AN: 2102

Alfa AF: 0.453 Hom.: 62799

Bravo AF: 0.446

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs366676; hg19: chr6-88717766;