rs928304

Variant names:

• chr21-44983144-C-T
• rs928304

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 0.226 in 151,954 control chromosomes in the GnomAD database, including 4,870 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 0.23 (4870 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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: 0.226 AC: 34372 AN: 151836 Hom.: 4870 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.226 AC: 34396 AN: 151954 Hom.: 4870 Cov.: 33 AF XY: 0.223 AC XY: 16554 AN XY: 74268

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.197

Alfa AF: 0.201 Hom.: 450

Bravo AF: 0.243

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.88
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928304; hg19: chr21-46403059; COSMIC: COSV53324833;