chr21-25558821-C-T

Variant names:

• chr21-25558821-C-T
• rs969885

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 0.085 in 152,096 control chromosomes in the GnomAD database, including 760 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 0.085 (760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.0849 AC: 12897 AN: 151978 Hom.: 752 Cov.: 31

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0850 AC: 12926 AN: 152096 Hom.: 760 Cov.: 31 AF XY: 0.0912 AC XY: 6781 AN XY: 74326

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0864

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0357 Hom.: 25

Bravo AF: 0.0815

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969885; hg19: chr21-26931133;