21-10809484-G-T

Variant names:

• chr21-10809484-G-T
• rs413191

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 0.042 (0 hom., cov: 220)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.0422 AC: 2751 AN: 65260 Hom.: 0 Cov.: 220

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.00694

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0347

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0300

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0420

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;InbreedingCoeff AF: 0.0422 AC: 2754 AN: 65324 Hom.: 0 Cov.: 220 AF XY: 0.0416 AC XY: 1381 AN XY: 33160

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

African (AFR) AF: 0.0643 AC: 1100 AN: 17110

American (AMR) AF: 0.0584 AC: 421 AN: 7212

Ashkenazi Jewish (ASJ) AF: 0.0347 AC: 47 AN: 1354

East Asian (EAS) AF: 0.0344 AC: 75 AN: 2178

South Asian (SAS) AF: 0.0349 AC: 77 AN: 2206

European-Finnish (FIN) AF: 0.0191 AC: 104 AN: 5434

Middle Eastern (MID) AF: 0.0208 AC: 2 AN: 96

European-Non Finnish (NFE) AF: 0.0313 AC: 888 AN: 28414

Other (OTH) AF: 0.0417 AC: 37 AN: 888

⚠️ 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: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.29

Splicing

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

Other links and lift over

dbSNP: rs413191; hg19: chr21-10702973;