21-9868128-G-A

Variant names:

• chr21-9868128-G-A
• rs376187

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 0.24 (2 hom., cov: 87)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=6.682).

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: 0.237 AC: 26542 AN: 111808 Hom.: 2 Cov.: 87

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.260

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: InbreedingCoeff AF: 0.237 AC: 26551 AN: 111920 Hom.: 2 Cov.: 87 AF XY: 0.236 AC XY: 12964 AN XY: 54890

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

African (AFR) AF: 0.111 AC: 3683 AN: 33260

American (AMR) AF: 0.281 AC: 2990 AN: 10648

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 815 AN: 2380

East Asian (EAS) AF: 0.0322 AC: 149 AN: 4624

South Asian (SAS) AF: 0.208 AC: 727 AN: 3500

European-Finnish (FIN) AF: 0.330 AC: 2516 AN: 7634

Middle Eastern (MID) AF: 0.304 AC: 62 AN: 204

European-Non Finnish (NFE) AF: 0.315 AC: 14961 AN: 47440

Other (OTH) AF: 0.254 AC: 403 AN: 1584

⚠️ 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: 0.268 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.7
PhyloP100		0.94

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: rs376187; hg19: chr4_gl000193_random-135442;