21-25852866-T-C

Variant names:

• chr21-25852866-T-C
• rs7282634

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 0.496 in 151,982 control chromosomes in the GnomAD database, including 19,186 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 0.50 (19186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.496 AC: 75286 AN: 151864 Hom.: 19154 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.496 AC: 75363 AN: 151982 Hom.: 19186 Cov.: 32 AF XY: 0.502 AC XY: 37256 AN XY: 74284

African (AFR) AF: 0.561 AC: 23268 AN: 41464

American (AMR) AF: 0.536 AC: 8183 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3557 AN: 5150

South Asian (SAS) AF: 0.600 AC: 2886 AN: 4812

European-Finnish (FIN) AF: 0.461 AC: 4867 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29461 AN: 67952

Other (OTH) AF: 0.486 AC: 1026 AN: 2110

Alfa AF: 0.457 Hom.: 8512

Bravo AF: 0.506

Asia WGS AF: 0.633 AC: 2197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.81
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7282634; hg19: chr21-27225177;