rs2829946

Variant names:

• chr21-25844046-C-T
• rs2829946

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 0.15 in 152,160 control chromosomes in the GnomAD database, including 1,843 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 (1843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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: 0.150 AC: 22860 AN: 152042 Hom.: 1837 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0910

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.150 AC: 22884 AN: 152160 Hom.: 1843 Cov.: 32 AF XY: 0.149 AC XY: 11094 AN XY: 74390

African (AFR) AF: 0.161 AC: 6690 AN: 41528

American (AMR) AF: 0.121 AC: 1853 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0910 AC: 315 AN: 3462

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5168

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4822

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11117 AN: 67984

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.155 Hom.: 4554

Bravo AF: 0.147

Asia WGS AF: 0.0600 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2829946; hg19: chr21-27216357;