21-33401191-T-TG

Variant names:

• chr21-33401191-T-TG
• rs17880053

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.246 in 152,032 control chromosomes in the GnomAD database, including 6,386 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6386 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

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: 0.246 AC: 37363 AN: 151914 Hom.: 6370 Cov.: 25

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.246 AC: 37416 AN: 152032 Hom.: 6386 Cov.: 25 AF XY: 0.247 AC XY: 18335 AN XY: 74320

African (AFR) AF: 0.466 AC: 19300 AN: 41432

American (AMR) AF: 0.177 AC: 2708 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2176 AN: 5156

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2006 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8841 AN: 67980

Other (OTH) AF: 0.198 AC: 420 AN: 2116

Alfa AF: 0.194 Hom.: 527

Bravo AF: 0.257

Asia WGS AF: 0.389 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17880053; hg19: chr21-34773497;