rs8127220

Positions:

• chr21-17409363-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.129 in 152,114 control chromosomes in the GnomAD database, including 2,347 homozygotes. 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 0.13 (2347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

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: 0.129 AC: 19549 AN: 151996 Hom.: 2334 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.129 AC: 19606 AN: 152114 Hom.: 2347 Cov.: 32 AF XY: 0.125 AC XY: 9262 AN XY: 74386

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0513

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0703 Hom.: 719

Bravo AF: 0.142

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8127220; hg19: chr21-18781682;