11-64322402-C-T

Variant names:

• chr11-64322402-C-T
• rs4930702

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 0.202 in 152,206 control chromosomes in the GnomAD database, including 3,749 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 0.20 (3749 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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: 0.202 AC: 30707 AN: 152088 Hom.: 3741 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.202 AC: 30755 AN: 152206 Hom.: 3749 Cov.: 33 AF XY: 0.204 AC XY: 15179 AN XY: 74402

African (AFR) AF: 0.260 AC: 10781 AN: 41542

American (AMR) AF: 0.278 AC: 4243 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2808 AN: 5170

South Asian (SAS) AF: 0.163 AC: 788 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1643 AN: 10590

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9295 AN: 68002

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.157 Hom.: 1157

Bravo AF: 0.218

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4930702; hg19: chr11-64089874;