6-88093881-C-T

Variant names:

• chr6-88093881-C-T
• rs806454

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 0.789 in 152,162 control chromosomes in the GnomAD database, including 47,663 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 (47663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119900 AN: 152044 Hom.: 47635 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.789 AC: 119987 AN: 152162 Hom.: 47663 Cov.: 32 AF XY: 0.797 AC XY: 59255 AN XY: 74392

African (AFR) AF: 0.727 AC: 30159 AN: 41466

American (AMR) AF: 0.841 AC: 12860 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2410 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5165 AN: 5188

South Asian (SAS) AF: 0.871 AC: 4198 AN: 4822

European-Finnish (FIN) AF: 0.877 AC: 9291 AN: 10596

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53250 AN: 68010

Other (OTH) AF: 0.791 AC: 1670 AN: 2112

Alfa AF: 0.778 Hom.: 95559

Bravo AF: 0.783

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.83
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs806454; hg19: chr6-88803599;