21-19368235-T-C

Variant names:

• chr21-19368235-T-C
• rs2825544

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 0.334 in 151,960 control chromosomes in the GnomAD database, including 8,697 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 0.33 (8697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50759 AN: 151840 Hom.: 8695 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.334 AC: 50780 AN: 151960 Hom.: 8697 Cov.: 32 AF XY: 0.332 AC XY: 24679 AN XY: 74298

African (AFR) AF: 0.333 AC: 13803 AN: 41456

American (AMR) AF: 0.342 AC: 5216 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1874 AN: 5172

South Asian (SAS) AF: 0.390 AC: 1884 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2911 AN: 10580

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22959 AN: 67884

Other (OTH) AF: 0.328 AC: 694 AN: 2114

Alfa AF: 0.334 Hom.: 12288

Bravo AF: 0.338

Asia WGS AF: 0.358 AC: 1242 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2825544; hg19: chr21-20740552;