21-25876118-C-T

Variant names:

• chr21-25876118-C-T
• rs2242682

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 0.364 in 151,330 control chromosomes in the GnomAD database, including 10,338 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 0.36 (10338 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.365 AC: 55120 AN: 151212 Hom.: 10332 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.364 AC: 55155 AN: 151330 Hom.: 10338 Cov.: 31 AF XY: 0.371 AC XY: 27403 AN XY: 73876

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.363

Alfa AF: 0.370 Hom.: 4278

Bravo AF: 0.357

Asia WGS AF: 0.447 AC: 1548 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2242682; hg19: chr21-27248429;