rs2307930

Variant names:

• chr6-83766659-A-AATGG
• rs2307930

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.187 in 152,106 control chromosomes in the GnomAD database, including 3,161 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3161 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 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: 0.187 AC: 28454 AN: 151988 Hom.: 3154 Cov.: 28

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.187 AC: 28474 AN: 152106 Hom.: 3161 Cov.: 28 AF XY: 0.190 AC XY: 14135 AN XY: 74354

African (AFR) AF: 0.142 AC: 5910 AN: 41528

American (AMR) AF: 0.316 AC: 4819 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2402 AN: 5146

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4816

European-Finnish (FIN) AF: 0.139 AC: 1472 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11401 AN: 67980

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.168 Hom.: 249

Bravo AF: 0.199

Asia WGS AF: 0.300 AC: 1045 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2307930;

hg19: chr6-84476378;