rs17880053

chr21-33401191-T-TG

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;