11-63145382-T-C

Variant names:

• chr11-63145382-T-C
• rs4366490

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 0.76 in 151,886 control chromosomes in the GnomAD database, including 45,467 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 0.76 (45467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115452 AN: 151768 Hom.: 45462 Cov.: 30

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.760 AC: 115485 AN: 151886 Hom.: 45467 Cov.: 30 AF XY: 0.763 AC XY: 56673 AN XY: 74242

African (AFR) AF: 0.536 AC: 22189 AN: 41368

American (AMR) AF: 0.831 AC: 12683 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4655 AN: 5162

South Asian (SAS) AF: 0.842 AC: 4049 AN: 4806

European-Finnish (FIN) AF: 0.882 AC: 9304 AN: 10552

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57300 AN: 67958

Other (OTH) AF: 0.789 AC: 1664 AN: 2108

Alfa AF: 0.725 Hom.: 2836

Bravo AF: 0.750

Asia WGS AF: 0.825 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.43
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4366490; hg19: chr11-62912854;