rs500254

Variant names:

• chr11-118808071-G-A
• rs500254

Your query was ambiguous. Multiple possible variants found:

• chr11-118808071-G-A
• chr11-118808071-G-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 0.847 in 152,052 control chromosomes in the GnomAD database, including 55,010 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 0.85 (55010 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.847 AC: 128737 AN: 151934 Hom.: 54968 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.847 AC: 128835 AN: 152052 Hom.: 55010 Cov.: 30 AF XY: 0.849 AC XY: 63122 AN XY: 74340

African (AFR) AF: 0.738 AC: 30595 AN: 41430

American (AMR) AF: 0.894 AC: 13658 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3140 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5160

South Asian (SAS) AF: 0.894 AC: 4306 AN: 4818

European-Finnish (FIN) AF: 0.898 AC: 9513 AN: 10596

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59567 AN: 68000

Other (OTH) AF: 0.860 AC: 1806 AN: 2100

Alfa AF: 0.864 Hom.: 9641

Bravo AF: 0.841

Asia WGS AF: 0.936 AC: 3256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.19
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs500254; hg19: chr11-118678780;