21-44985376-C-T

Variant names:

• chr21-44985376-C-T
• rs928310

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;