11-23445820-T-A

Variant names:

• chr11-23445820-T-A
• rs28891168

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.75 (24551 hom., cov: 12)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.750 AC: 62493 AN: 83356 Hom.: 24549 Cov.: 12

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.706

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.750 AC: 62511 AN: 83382 Hom.: 24551 Cov.: 12 AF XY: 0.737 AC XY: 28433 AN XY: 38570

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.594 AC: 13865 AN: 23330

American (AMR) AF: 0.686 AC: 5239 AN: 7634

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 1717 AN: 2148

East Asian (EAS) AF: 0.993 AC: 2531 AN: 2550

South Asian (SAS) AF: 0.831 AC: 1563 AN: 1880

European-Finnish (FIN) AF: 0.751 AC: 3457 AN: 4604

Middle Eastern (MID) AF: 0.799 AC: 155 AN: 194

European-Non Finnish (NFE) AF: 0.833 AC: 32747 AN: 39334

Other (OTH) AF: 0.710 AC: 778 AN: 1096

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.826 Hom.: 5681

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs28891168; hg19: chr11-23467366;