rs2254546

Variant names:

• chr8-11486171-A-G
• rs2254546

Your query was ambiguous. Multiple possible variants found:

• chr8-11486171-A-G
• chr8-11486171-A-T

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 0.831 in 151,962 control chromosomes in the GnomAD database, including 52,673 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 0.83 (52673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.857 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: 0.831 AC: 126156 AN: 151844 Hom.: 52618 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.831 AC: 126269 AN: 151962 Hom.: 52673 Cov.: 31 AF XY: 0.823 AC XY: 61162 AN XY: 74276

African (AFR) AF: 0.861 AC: 35718 AN: 41496

American (AMR) AF: 0.870 AC: 13304 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2892 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3821 AN: 5150

South Asian (SAS) AF: 0.796 AC: 3827 AN: 4810

European-Finnish (FIN) AF: 0.691 AC: 7277 AN: 10536

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56827 AN: 67894

Other (OTH) AF: 0.827 AC: 1739 AN: 2104

Alfa AF: 0.838 Hom.: 166175

Bravo AF: 0.846

Asia WGS AF: 0.805 AC: 2798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2254546; hg19: chr8-11343680;