rs2823455

Variant names:

• chr21-15696847-C-T
• rs2823455

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 0.149 in 152,182 control chromosomes in the GnomAD database, including 2,315 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 0.15 (2315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.149 AC: 22673 AN: 152064 Hom.: 2310 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0935

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.149 AC: 22704 AN: 152182 Hom.: 2315 Cov.: 32 AF XY: 0.148 AC XY: 10983 AN XY: 74416

African (AFR) AF: 0.291 AC: 12065 AN: 41496

American (AMR) AF: 0.101 AC: 1552 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 324 AN: 3466

East Asian (EAS) AF: 0.0890 AC: 462 AN: 5190

South Asian (SAS) AF: 0.0493 AC: 238 AN: 4826

European-Finnish (FIN) AF: 0.123 AC: 1304 AN: 10590

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

European-Non Finnish (NFE) AF: 0.0938 AC: 6376 AN: 68004

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.112 Hom.: 4051

Bravo AF: 0.155

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.54
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs2823455; hg19: chr21-17069166;