chr6-99107880-A-G

Variant names:

• chr6-99107880-A-G
• rs6905786

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 0.592 in 152,004 control chromosomes in the GnomAD database, including 26,854 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 0.59 (26854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 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: 0.592 AC: 89892 AN: 151888 Hom.: 26830 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.592 AC: 89966 AN: 152004 Hom.: 26854 Cov.: 32 AF XY: 0.594 AC XY: 44099 AN XY: 74296

African (AFR) AF: 0.552 AC: 22886 AN: 41458

American (AMR) AF: 0.550 AC: 8404 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2060 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3237 AN: 5148

South Asian (SAS) AF: 0.618 AC: 2978 AN: 4816

European-Finnish (FIN) AF: 0.642 AC: 6793 AN: 10584

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41524 AN: 67928

Other (OTH) AF: 0.610 AC: 1289 AN: 2114

Alfa AF: 0.603 Hom.: 17262

Bravo AF: 0.583

Asia WGS AF: 0.659 AC: 2293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.46
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6905786; hg19: chr6-99555756;