rs1839699

Variant names:

• chr21-9753938-G-A
• rs1839699

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 0.77 (40407 hom., cov: 77)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.663).

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: 0.765 AC: 116472 AN: 152236 Hom.: 40354 Cov.: 77

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.766

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: 0.765 AC: 116584 AN: 152354 Hom.: 40407 Cov.: 77 AF XY: 0.769 AC XY: 57311 AN XY: 74512

African (AFR) AF: 0.819 AC: 34041 AN: 41578

American (AMR) AF: 0.727 AC: 11129 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2608 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4220 AN: 5192

South Asian (SAS) AF: 0.861 AC: 4164 AN: 4834

European-Finnish (FIN) AF: 0.788 AC: 8367 AN: 10618

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49525 AN: 68030

Other (OTH) AF: 0.768 AC: 1624 AN: 2114

Alfa AF: 0.780 Hom.: 3321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.7
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1839699; hg19: chr4_gl000193_random-21252;