rs2825300

Variant names:

• chr21-19034265-A-C
• rs2825300

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0236 in 152,344 control chromosomes in the GnomAD database, including 61 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 0.024 (61 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0236 (3595/152344) while in subpopulation NFE AF = 0.0373 (2537/68024). AF 95% confidence interval is 0.0361. There are 61 homozygotes in GnomAd4. There are 1779 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 61 gene

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: 0.0236 AC: 3596 AN: 152226 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00632

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0150

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0236 AC: 3595 AN: 152344 Hom.: 61 Cov.: 32 AF XY: 0.0239 AC XY: 1779 AN XY: 74496

African (AFR) AF: 0.00630 AC: 262 AN: 41586

American (AMR) AF: 0.0150 AC: 229 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 63 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4828

European-Finnish (FIN) AF: 0.0284 AC: 302 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2537 AN: 68024

Other (OTH) AF: 0.0194 AC: 41 AN: 2116

Alfa AF: 0.0319 Hom.: 58

Bravo AF: 0.0208

Asia WGS AF: 0.00751 AC: 26 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	5.2
DANN	Benign	0.72
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2825300; hg19: chr21-20406584;