chr11-59382169-T-A

Variant names:

• chr11-59382169-T-A
• rs4939287

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 0.23 in 152,068 control chromosomes in the GnomAD database, including 4,935 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 0.23 (4935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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: 0.230 AC: 34943 AN: 151950 Hom.: 4939 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.230 AC: 34932 AN: 152068 Hom.: 4935 Cov.: 31 AF XY: 0.231 AC XY: 17138 AN XY: 74314

African (AFR) AF: 0.0602 AC: 2499 AN: 41508

American (AMR) AF: 0.310 AC: 4732 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3466

East Asian (EAS) AF: 0.155 AC: 799 AN: 5170

South Asian (SAS) AF: 0.248 AC: 1192 AN: 4812

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10558

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20767 AN: 67966

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.142 Hom.: 280

Bravo AF: 0.224

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.32
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4939287; hg19: chr11-59149642;