21-44985427-A-G

Position:

• chr21-44985427-A-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 0.557 in 152,106 control chromosomes in the GnomAD database, including 24,767 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 0.56 (24767 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84712 AN: 151988 Hom.: 24759 Cov.: 34

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.557 AC: 84755 AN: 152106 Hom.: 24767 Cov.: 34 AF XY: 0.561 AC XY: 41686 AN XY: 74364

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.593

Alfa AF: 0.587 Hom.: 3355

Bravo AF: 0.538

Asia WGS AF: 0.721 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928311; hg19: chr21-46405342;