chr21-46025877-A-G

Variant names:

• chr21-46025877-A-G
• rs4293630

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 0.14 in 152,244 control chromosomes in the GnomAD database, including 1,590 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 0.14 (1590 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21363 AN: 152124 Hom.: 1585 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.140 AC: 21374 AN: 152244 Hom.: 1590 Cov.: 33 AF XY: 0.138 AC XY: 10294 AN XY: 74436

African (AFR) AF: 0.151 AC: 6292 AN: 41534

American (AMR) AF: 0.103 AC: 1575 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.0886 AC: 460 AN: 5192

South Asian (SAS) AF: 0.196 AC: 943 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1282 AN: 10598

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9669 AN: 68004

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.141 Hom.: 6960

Bravo AF: 0.138

Asia WGS AF: 0.159 AC: 553 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.76
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4293630; hg19: chr21-47445791; COSMIC: COSV69598238;