21-26344335-C-T

Variant names:

• chr21-26344335-C-T
• rs9975851

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 0.554 in 151,748 control chromosomes in the GnomAD database, including 23,672 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 0.55 (23672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.554 AC: 84019 AN: 151628 Hom.: 23654 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.554 AC: 84073 AN: 151748 Hom.: 23672 Cov.: 32 AF XY: 0.558 AC XY: 41409 AN XY: 74148

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.554

Alfa AF: 0.559 Hom.: 3109

Bravo AF: 0.541

Asia WGS AF: 0.699 AC: 2421 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9975851; hg19: chr21-27716654;