21-44983243-G-A

Variant names:

• chr21-44983243-G-A
• rs928306

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.502 in 151,982 control chromosomes in the GnomAD database, including 22,202 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 0.50 (22202 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 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: 0.502 AC: 76202 AN: 151864 Hom.: 22201 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.502 AC: 76220 AN: 151982 Hom.: 22202 Cov.: 33 AF XY: 0.507 AC XY: 37666 AN XY: 74256

African (AFR) AF: 0.187 AC: 7757 AN: 41462

American (AMR) AF: 0.538 AC: 8221 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1931 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3715 AN: 5154

South Asian (SAS) AF: 0.764 AC: 3673 AN: 4808

European-Finnish (FIN) AF: 0.635 AC: 6702 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42370 AN: 67944

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.576 Hom.: 9001

Bravo AF: 0.475

Asia WGS AF: 0.710 AC: 2464 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	1.8
DANN	Benign	0.61
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs928306; hg19: chr21-46403158;