rs928304

Positions:

• chr21-44983144-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 0.226 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;