chr21-15714437-A-G

Variant names:

• chr21-15714437-A-G
• rs2823460

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 0.129 in 150,126 control chromosomes in the GnomAD database, including 1,451 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 0.13 (1451 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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: 0.129 AC: 19388 AN: 150008 Hom.: 1448 Cov.: 30

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0883

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.129 AC: 19414 AN: 150126 Hom.: 1451 Cov.: 30 AF XY: 0.129 AC XY: 9473 AN XY: 73262

African (AFR) AF: 0.209 AC: 8471 AN: 40498

American (AMR) AF: 0.101 AC: 1515 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3456

East Asian (EAS) AF: 0.101 AC: 516 AN: 5122

South Asian (SAS) AF: 0.0710 AC: 339 AN: 4774

European-Finnish (FIN) AF: 0.142 AC: 1449 AN: 10216

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0936 AC: 6341 AN: 67746

Other (OTH) AF: 0.109 AC: 227 AN: 2076

Alfa AF: 0.108 Hom.: 445

Bravo AF: 0.128

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0020
DANN	Benign	0.22
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2823460; hg19: chr21-17086756;