rs2825300

chr21-19034265-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 61 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00630

Gnomad4 AMR AF: 0.0150

Gnomad4 ASJ AF: 0.0181

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0323 Hom.: 39

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2825300; hg19: chr21-20406584;