21-20299690-G-C

Variant names:

• chr21-20299690-G-C
• rs1487933

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.298 AC: 12342 AN: 41372

American (AMR) AF: 0.482 AC: 7343 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2828 AN: 5118

South Asian (SAS) AF: 0.520 AC: 2505 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6736 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41096 AN: 67936

Other (OTH) AF: 0.510 AC: 1080 AN: 2116

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1487933; hg19: chr21-21672002;