rs2838551

Variant names:

• chr21-44344514-T-G
• rs2838551

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 0.467 in 152,004 control chromosomes in the GnomAD database, including 18,488 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 0.47 (18488 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.467 AC: 70966 AN: 151890 Hom.: 18456 Cov.: 34

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.467 AC: 71061 AN: 152004 Hom.: 18488 Cov.: 34 AF XY: 0.466 AC XY: 34625 AN XY: 74264

African (AFR) AF: 0.712 AC: 29539 AN: 41502

American (AMR) AF: 0.409 AC: 6249 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1104 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1366 AN: 5156

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4826

European-Finnish (FIN) AF: 0.407 AC: 4289 AN: 10528

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24884 AN: 67940

Other (OTH) AF: 0.425 AC: 896 AN: 2106

Alfa AF: 0.400 Hom.: 48607

Bravo AF: 0.478

Asia WGS AF: 0.413 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs2838551; hg19: chr21-45764397;