rs2838566

Positions:

• chr21-44468699-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 0.0942 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.00497

Gnomad4 NFE AF: 0.00186

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0433 Hom.: 275

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838566; hg19: chr21-45888582;