21-44981252-T-G

Variant names:

• chr21-44981252-T-G
• rs914202

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 0.804 in 152,238 control chromosomes in the GnomAD database, including 49,370 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 (49370 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 0.804 AC: 122349 AN: 152120 Hom.: 49330 Cov.: 35

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.804 AC: 122448 AN: 152238 Hom.: 49370 Cov.: 35 AF XY: 0.804 AC XY: 59856 AN XY: 74450

African (AFR) AF: 0.837 AC: 34767 AN: 41544

American (AMR) AF: 0.817 AC: 12496 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2612 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4437 AN: 5170

South Asian (SAS) AF: 0.831 AC: 4014 AN: 4832

European-Finnish (FIN) AF: 0.790 AC: 8388 AN: 10622

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53125 AN: 67980

Other (OTH) AF: 0.803 AC: 1697 AN: 2114

Alfa AF: 0.800 Hom.: 6070

Bravo AF: 0.805

Asia WGS AF: 0.859 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs914202; hg19: chr21-46401167;