chr11-64584249-C-T

Variant names:

• chr11-64584249-C-T
• rs528211

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 0.448 in 151,846 control chromosomes in the GnomAD database, including 17,300 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 0.45 (17300 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.447 AC: 67885 AN: 151728 Hom.: 17284 Cov.: 30

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.448 AC: 67959 AN: 151846 Hom.: 17300 Cov.: 30 AF XY: 0.456 AC XY: 33836 AN XY: 74206

African (AFR) AF: 0.667 AC: 27588 AN: 41390

American (AMR) AF: 0.474 AC: 7251 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3472

East Asian (EAS) AF: 0.777 AC: 3987 AN: 5132

South Asian (SAS) AF: 0.425 AC: 2042 AN: 4802

European-Finnish (FIN) AF: 0.428 AC: 4515 AN: 10554

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20465 AN: 67902

Other (OTH) AF: 0.415 AC: 874 AN: 2104

Alfa AF: 0.343 Hom.: 12950

Bravo AF: 0.462

Asia WGS AF: 0.606 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs528211; hg19: chr11-64351721;