21-44881827-A-G

Variant names:

• chr21-44881827-A-G
• rs440555

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 0.698 in 152,162 control chromosomes in the GnomAD database, including 38,382 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 0.70 (38382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 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: 0.697 AC: 106016 AN: 152044 Hom.: 38316 Cov.: 33

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.698 AC: 106147 AN: 152162 Hom.: 38382 Cov.: 33 AF XY: 0.697 AC XY: 51866 AN XY: 74368

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.707

Alfa AF: 0.643 Hom.: 4044

Bravo AF: 0.708

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs440555; hg19: chr21-46301742;