21-42308924-C-T

Variant names:

• chr21-42308924-C-T
• rs225436

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 0.603 in 152,158 control chromosomes in the GnomAD database, including 29,767 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 0.60 (29767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.603 AC: 91632 AN: 152040 Hom.: 29727 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.603 AC: 91732 AN: 152158 Hom.: 29767 Cov.: 32 AF XY: 0.594 AC XY: 44156 AN XY: 74384

African (AFR) AF: 0.837 AC: 34786 AN: 41544

American (AMR) AF: 0.519 AC: 7929 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3470

East Asian (EAS) AF: 0.188 AC: 971 AN: 5160

South Asian (SAS) AF: 0.447 AC: 2155 AN: 4824

European-Finnish (FIN) AF: 0.485 AC: 5126 AN: 10572

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36683 AN: 67996

Other (OTH) AF: 0.591 AC: 1248 AN: 2110

Alfa AF: 0.556 Hom.: 55262

Bravo AF: 0.615

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs225436; hg19: chr21-43729034;