rs1487933

chr21-20299690-G-Cchr21-20299690-G-Tchr21-20299690-G-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 0.505 in 151,808 control chromosomes in the GnomAD database, including 20,759 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 (20759 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.505 AC: 76575 AN: 151688 Hom.: 20748 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.505 AC: 76607 AN: 151808 Hom.: 20759 Cov.: 31 AF XY: 0.507 AC XY: 37620 AN XY: 74154

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.510

Alfa AF: 0.447 Hom.: 1454

Bravo AF: 0.479

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.39
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487933; hg19: chr21-21672002;