rs17880053

Variant names:

• chr21-33401191-T-TG
• rs17880053

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.198

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17880053; hg19: chr21-34773497;