11-60864668-C-T

Variant names:

• chr11-60864668-C-T
• rs530880

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 0.194 in 151,976 control chromosomes in the GnomAD database, including 3,733 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 0.19 (3733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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: 0.194 AC: 29455 AN: 151858 Hom.: 3731 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.194 AC: 29457 AN: 151976 Hom.: 3733 Cov.: 32 AF XY: 0.187 AC XY: 13902 AN XY: 74298

African (AFR) AF: 0.0518 AC: 2147 AN: 41448

American (AMR) AF: 0.184 AC: 2819 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3468

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5176

South Asian (SAS) AF: 0.0848 AC: 408 AN: 4814

European-Finnish (FIN) AF: 0.230 AC: 2422 AN: 10540

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19293 AN: 67936

Other (OTH) AF: 0.223 AC: 469 AN: 2104

Alfa AF: 0.237 Hom.: 798

Bravo AF: 0.187

Asia WGS AF: 0.0680 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs530880; hg19: chr11-60632141;