rs9975851

chr21-26344335-C-Tchr21-26344335-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;