chr21-42329090-T-C

Variant names:

• chr21-42329090-T-C
• rs9982439

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 0.0306 in 152,230 control chromosomes in the GnomAD database, including 83 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 0.031 (83 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0306 (4655/152230) while in subpopulation NFE AF = 0.0369 (2513/68014). AF 95% confidence interval is 0.0357. There are 83 homozygotes in GnomAd4. There are 2174 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 83 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: 0.0306 AC: 4651 AN: 152112 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0306 AC: 4655 AN: 152230 Hom.: 83 Cov.: 32 AF XY: 0.0292 AC XY: 2174 AN XY: 74448

African (AFR) AF: 0.0303 AC: 1256 AN: 41498

American (AMR) AF: 0.0226 AC: 346 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4820

European-Finnish (FIN) AF: 0.0193 AC: 205 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0369 AC: 2513 AN: 68014

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0355 Hom.: 85

Bravo AF: 0.0310

Asia WGS AF: 0.0120 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.51
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9982439; hg19: chr21-43749200;