rs9982492

chr21-14363354-T-Cchr21-14363354-T-A

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 0.768 in 152,156 control chromosomes in the GnomAD database, including 45,385 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 0.77 (45385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116827 AN: 152038 Hom.: 45351 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.768 AC: 116908 AN: 152156 Hom.: 45385 Cov.: 32 AF XY: 0.763 AC XY: 56757 AN XY: 74378

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.755

Alfa AF: 0.758 Hom.: 55090

Bravo AF: 0.763

Asia WGS AF: 0.664 AC: 2308 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	3.8
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9982492; hg19: chr21-15735675;