rs1839699

Positions:

• chr21-9753938-G-A

Variant summary

Our verdict is Likely benign. Variant got -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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 116472 AN: 152236 Hom.: 40354 Cov.: 77 FAILED QC

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

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.768

Alfa AF: 0.780 Hom.: 3321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1839699; hg19: chr4_gl000193_random-21252;