rs1735884

Positions:

• chr21-20448096-C-T

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 0.769 in 151,980 control chromosomes in the GnomAD database, including 45,093 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 0.77 (45093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.769 AC: 116760 AN: 151866 Hom.: 45083 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.769 AC: 116819 AN: 151980 Hom.: 45093 Cov.: 32 AF XY: 0.772 AC XY: 57318 AN XY: 74286

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.770

Alfa AF: 0.775 Hom.: 65119

Bravo AF: 0.765

Asia WGS AF: 0.802 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1735884; hg19: chr21-21820408;