chr21-16650886-C-T

Position:

• chr21-16650886-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0989 in 152,218 control chromosomes in the GnomAD database, including 1,930 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 0.099 (1930 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 15001 AN: 152100 Hom.: 1917 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0989 AC: 15049 AN: 152218 Hom.: 1930 Cov.: 33 AF XY: 0.0978 AC XY: 7283 AN XY: 74442

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.00301

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0256 Hom.: 542

Bravo AF: 0.109

Asia WGS AF: 0.126 AC: 439 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	0.33
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305777; hg19: chr21-18023205;