21-44981213-T-G

Variant names:

• chr21-44981213-T-G
• rs914200

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 0.803 in 152,120 control chromosomes in the GnomAD database, including 49,173 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 0.80 (49173 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.803 AC: 122070 AN: 152002 Hom.: 49134 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.803 AC: 122168 AN: 152120 Hom.: 49173 Cov.: 33 AF XY: 0.803 AC XY: 59689 AN XY: 74364

African (AFR) AF: 0.836 AC: 34703 AN: 41508

American (AMR) AF: 0.816 AC: 12475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2615 AN: 3468

East Asian (EAS) AF: 0.858 AC: 4427 AN: 5158

South Asian (SAS) AF: 0.828 AC: 3999 AN: 4832

European-Finnish (FIN) AF: 0.789 AC: 8353 AN: 10588

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 52992 AN: 67958

Other (OTH) AF: 0.801 AC: 1693 AN: 2114

Alfa AF: 0.748 Hom.: 2283

Bravo AF: 0.804

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs914200; hg19: chr21-46401128;