rs928304

Variant names:

• chr21-44983144-C-T
• rs928304

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 0.226 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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

African (AFR) AF: 0.398 AC: 16476 AN: 41422

American (AMR) AF: 0.244 AC: 3722 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3470

East Asian (EAS) AF: 0.109 AC: 560 AN: 5142

South Asian (SAS) AF: 0.0571 AC: 275 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1626 AN: 10564

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10430 AN: 67950

Other (OTH) AF: 0.197 AC: 415 AN: 2106

Alfa AF: 0.208 Hom.: 506

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

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