rs928254

Variant names:

• chr21-19712123-G-A
• rs928254

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 0.333 in 151,768 control chromosomes in the GnomAD database, including 8,626 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 0.33 (8626 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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: 0.333 AC: 50523 AN: 151650 Hom.: 8623 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.333 AC: 50548 AN: 151768 Hom.: 8626 Cov.: 33 AF XY: 0.327 AC XY: 24274 AN XY: 74166

African (AFR) AF: 0.369 AC: 15287 AN: 41394

American (AMR) AF: 0.260 AC: 3957 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1219 AN: 3464

East Asian (EAS) AF: 0.332 AC: 1708 AN: 5144

South Asian (SAS) AF: 0.404 AC: 1947 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2409 AN: 10508

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22940 AN: 67888

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.331 Hom.: 1062

Bravo AF: 0.332

Asia WGS AF: 0.367 AC: 1276 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.39
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs928254; hg19: chr21-21084437;