rs2838566

Variant names:

• chr21-44468699-C-T
• rs2838566

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 0.0942 in 148,054 control chromosomes in the GnomAD database, including 1,876 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 0.094 (1876 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.0939 AC: 13904 AN: 148012 Hom.: 1867 Cov.: 27

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.00497

Gnomad MID AF: 0.0490

Gnomad NFE AF: 0.00188

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0942 AC: 13944 AN: 148054 Hom.: 1876 Cov.: 27 AF XY: 0.0933 AC XY: 6709 AN XY: 71888

African (AFR) AF: 0.295 AC: 11713 AN: 39752

American (AMR) AF: 0.0850 AC: 1258 AN: 14798

Ashkenazi Jewish (ASJ) AF: 0.000290 AC: 1 AN: 3452

East Asian (EAS) AF: 0.0763 AC: 388 AN: 5084

South Asian (SAS) AF: 0.0516 AC: 242 AN: 4692

European-Finnish (FIN) AF: 0.00497 AC: 47 AN: 9454

Middle Eastern (MID) AF: 0.0536 AC: 15 AN: 280

European-Non Finnish (NFE) AF: 0.00186 AC: 126 AN: 67572

Other (OTH) AF: 0.0748 AC: 154 AN: 2058

Alfa AF: 0.0425 Hom.: 318

Bravo AF: 0.113

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.55
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2838566; hg19: chr21-45888582;