chr21-16916765-C-T

Variant names:

• chr21-16916765-C-T
• rs2824129

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 0.449 in 151,626 control chromosomes in the GnomAD database, including 16,170 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 0.45 (16170 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.449 AC: 67984 AN: 151508 Hom.: 16153 Cov.: 30

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.449 AC: 68039 AN: 151626 Hom.: 16170 Cov.: 30 AF XY: 0.450 AC XY: 33375 AN XY: 74092

African (AFR) AF: 0.604 AC: 24939 AN: 41264

American (AMR) AF: 0.495 AC: 7541 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2717 AN: 5112

South Asian (SAS) AF: 0.342 AC: 1641 AN: 4796

European-Finnish (FIN) AF: 0.383 AC: 4043 AN: 10550

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.364 AC: 24723 AN: 67882

Other (OTH) AF: 0.434 AC: 917 AN: 2112

Alfa AF: 0.828 Hom.: 24578

Bravo AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2824129; hg19: chr21-18289085;