21-14363354-T-C

Variant names:

• chr21-14363354-T-C
• rs9982492

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 0.768 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.846 AC: 35107 AN: 41504

American (AMR) AF: 0.652 AC: 9955 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2790 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3200 AN: 5168

South Asian (SAS) AF: 0.691 AC: 3333 AN: 4826

European-Finnish (FIN) AF: 0.732 AC: 7752 AN: 10588

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52233 AN: 68008

Other (OTH) AF: 0.755 AC: 1591 AN: 2108

Alfa AF: 0.760 Hom.: 70775

Bravo AF: 0.763

Asia WGS AF: 0.664 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9982492; hg19: chr21-15735675;