rs928310

chr21-44985376-C-Tchr21-44985376-C-G

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 0.505 in 152,162 control chromosomes in the GnomAD database, including 22,461 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 0.51 (22461 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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 (SAS) allele frequency at 95% confidence interval = 0.746 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: 0.506 AC: 76888 AN: 152044 Hom.: 22462 Cov.: 34

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.505 AC: 76905 AN: 152162 Hom.: 22461 Cov.: 34 AF XY: 0.511 AC XY: 38029 AN XY: 74400

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.556

Alfa AF: 0.435 Hom.: 1455

Bravo AF: 0.479

Asia WGS AF: 0.711 AC: 2470 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	0.85
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928310; hg19: chr21-46405291;