rs6731289

Variant names:

• chr2-82665670-C-A
• rs6731289

Your query was ambiguous. Multiple possible variants found:

• chr2-82665670-C-A
• chr2-82665670-C-G

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 0.43 in 151,872 control chromosomes in the GnomAD database, including 19,246 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 0.43 (19246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.430 AC: 65204 AN: 151752 Hom.: 19186 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.430 AC: 65335 AN: 151872 Hom.: 19246 Cov.: 32 AF XY: 0.424 AC XY: 31482 AN XY: 74226

African (AFR) AF: 0.844 AC: 34975 AN: 41450

American (AMR) AF: 0.345 AC: 5251 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5162

South Asian (SAS) AF: 0.251 AC: 1213 AN: 4824

European-Finnish (FIN) AF: 0.233 AC: 2456 AN: 10562

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17752 AN: 67890

Other (OTH) AF: 0.387 AC: 815 AN: 2104

Alfa AF: 0.313 Hom.: 31915

Bravo AF: 0.457

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6731289; hg19: chr2-82892794;