21-24686059-G-T

Variant names:

• chr21-24686059-G-T
• rs2298515

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 0.0437 in 152,104 control chromosomes in the GnomAD database, including 263 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 0.044 (263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.0437 AC: 6636 AN: 151984 Hom.: 263 Cov.: 32

Gnomad AFR AF: 0.00775

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0437 AC: 6640 AN: 152104 Hom.: 263 Cov.: 32 AF XY: 0.0485 AC XY: 3606 AN XY: 74346

African (AFR) AF: 0.00775 AC: 322 AN: 41530

American (AMR) AF: 0.0468 AC: 714 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 435 AN: 3462

East Asian (EAS) AF: 0.104 AC: 537 AN: 5182

South Asian (SAS) AF: 0.206 AC: 992 AN: 4822

European-Finnish (FIN) AF: 0.0577 AC: 611 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0417 AC: 2833 AN: 67950

Other (OTH) AF: 0.0593 AC: 125 AN: 2108

Alfa AF: 0.0466 Hom.: 543

Bravo AF: 0.0386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs2298515; hg19: chr21-26058373;