21-25852866-T-C

Position:

• chr21-25852866-T-C

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 0.496 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.496 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

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.486

Alfa AF: 0.456 Hom.: 7587

Bravo AF: 0.506

Asia WGS AF: 0.633 AC: 2197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7282634; hg19: chr21-27225177;